Publications

I have published 41 papers in peer reviewed conferences and journals. Below you will find a complete listing of all my contributions (100) to conferences, journals, workshops, proceedings, and technical recommendations, as well as my PhD Thesis.

You can also find my publications on the following academic repositories.

2023

1. FAIR in action - a flexible framework to guide FAIRification
   Welter, Danielle and Juty, Nick and Rocca-Serra, Philippe and Xu, Fuqi and Henderson, David and Gu, Wei and Strubel, Jolanda and Giessmann, Robert and Emam, Ibrahim and Gadiya, Yojana and Abbassi-Daloii, Tooba and Alharbi, Ebtisam and Gray, Alasdair and Courtot, Melanie and Gribbon, Philip and Ioannidis, Vassilios and Reilly, Dorothy and Lynch, Nick and Boiten, Jan-Willem and Satagopam, Venkata and Goble, Carole and Sansone, Susanna-Assunta and Burdett, Tony
   Scientific Data, Nature, 2023
   To appear
   

   The COVID-19 pandemic has highlighted the need for FAIR (Findable, Accessible, Interoperable, and Reusable) data more than any other scientific challenge to date. We developed a flexible, multi-level, domain-agnostic FAIRification framework, providing practical guidance to improve the FAIRness for both existing and future clinical and molecular datasets. We validated the framework in collaboration with a wide range of public-private partnership projects, demonstrating and implementing improvements across all aspects of FAIR, using a variety of datasets, to demonstrate the reproducibility and wide-ranging applicability of this framework for intra-project FAIRification.

   @article{Welter:FAIR-in-action:SDATA2023,
     title = {{FAIR} in action - a flexible framework to guide {FAIRification}},
     author = {Welter, Danielle and Juty, Nick and Rocca-Serra, Philippe and Xu, Fuqi and Henderson, David and Gu, Wei and Strubel, Jolanda and Giessmann, Robert and Emam, Ibrahim and Gadiya, Yojana and Abbassi-Daloii, Tooba and Alharbi, Ebtisam and Gray, Alasdair and Courtot, Melanie and Gribbon, Philip and Ioannidis, Vassilios and Reilly, Dorothy and Lynch, Nick and Boiten, Jan-Willem and Satagopam, Venkata and Goble, Carole and Sansone, Susanna-Assunta and Burdett, Tony},
     journal = {Scientific Data},
     optmonth = {},
     optvolume = {},
     year = {2023},
     doi = {10.5281/zenodo.7702124},
     url = {https://doi.org/10.5281/zenodo.7702124},
     publisher = {Nature},
     note = {To appear}
   }
   

2022

1. An ETL pipeline to construct the Intrinsically Disordered Proteins Knowledge Graph (IDP-KG) using Bioschemas JSON-LD data dumps
   Ammar, Ammar and Mičetić, Ivan and Gray, Alasdair J. G.
   Technical Report. BioHackrXiv. nov, 2022
   

   Schema.org and Bioschemas are lightweight vocabularies that aim at making the contents of web pages machine-readable so that software agents can consume that content and understand it in an actionable way. Due to the time needed to process each page, extracting markup by visiting each page of a site is not practical for huge sites. This approach imposes processing requirements on the publisher and the consumer. The Schema.org community proposed a method for exchanging markup from various pages as a DataFeed published at a recognized address in February 2022. This would ease publisher and customer processing requirements and accelerate data collection. In this work, we report on the implementation of a JSON-LD consumer ETL (Extract-Transform-Load) pipeline that enables data dumps to be ingested into knowledge graphs (KG). The pipeline loads scraped JSON-LD from the three sources, converts it to RDF, applies SPARQL construct queries to map the source RDF to a unified Bioschemas-based model and stores the resulting KG as a turtle file. This work was conducted during the one-week Biohackathion Europe 2022 in Paris France, under Project 23 titled, “Publishing and Consuming Schema.org DataFeeds.”

   @techreport{ammar:data-pipeline:biohackrxiv2022,
     title = {An ETL pipeline to construct the Intrinsically Disordered Proteins Knowledge Graph (IDP-KG) using Bioschemas JSON-LD data dumps},
     url = {https://biohackrxiv.org/7f95d/},
     doi = {10.37044/osf.io/7f95d},
     publisher = {BioHackrXiv},
     author = {Ammar, Ammar and Mičetić, Ivan and Gray, Alasdair J. G.},
     year = {2022},
     month = nov
   }
   
2. A Simple Standard for Sharing Ontological Mappings (SSSOM)
   Matentzoglu, Nicolas and Balhoff, James P and Bello, Susan M and Bizon, Chris and Brush, Matthew and Callahan, Tiffany J and Chute, Christopher G and Duncan, William D and Evelo, Chris T and Gabriel, Davera and others
   Database, 2022, Oxford Academic, 2022
   

   Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

   @article{nico:SSSOM:Database2022,
     title = {A Simple Standard for Sharing Ontological Mappings (SSSOM)},
     author = {Matentzoglu, Nicolas and Balhoff, James P and Bello, Susan M and Bizon, Chris and Brush, Matthew and Callahan, Tiffany J and Chute, Christopher G and Duncan, William D and Evelo, Chris T and Gabriel, Davera and others},
     journal = {Database},
     month = may,
     volume = {2022},
     year = {2022},
     doi = {10.1093/database/baac035},
     url = {https://doi.org/10.1093/database/baac035},
     publisher = {Oxford Academic}
   }
   
3. ELIXIR biovalidator for semantic validation of life science metadata
   Liyanage, Isuru and Burdett, Tony and Droesbeke, Bert and Erdos, Karoly and Fernandez, Rolando and Gray, Alasdair and Haseeb, Muhammad and Jupp, Simon and Penim, Flavia and Pommier, Cyril and Rocca-Serra, Philippe and Courtot, Mélanie and Coppens, Frederik
   Bioinformatics, 38(11):3141-3142, Oxford University Press, 2022
   btac195
   

   To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents.Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate

   @article{courtot:elixir-validator:bioinformatics2022,
     author = {Liyanage, Isuru and Burdett, Tony and Droesbeke, Bert and Erdos, Karoly and Fernandez, Rolando and Gray, Alasdair and Haseeb, Muhammad and Jupp, Simon and Penim, Flavia and Pommier, Cyril and Rocca-Serra, Philippe and Courtot, Mélanie and Coppens, Frederik},
     title = {{ELIXIR biovalidator for semantic validation of life science metadata}},
     journal = {Bioinformatics},
     year = {2022},
     month = apr,
     volume = {38},
     number = {11},
     pages = {3141-3142},
     publisher = {Oxford University Press},
     issn = {1367-4803},
     doi = {10.1093/bioinformatics/btac195},
     url = {https://doi.org/10.1093/bioinformatics/btac195},
     note = {btac195},
     eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac195/43287005/btac195.pdf}
   }
   
4. The FAIR Cookbook
   Rocca-Serra, Philippe and J G Gray, Alasdair and Delfin Rossaro, Alejandra and Splendiani, Andrea and Zaliani, Andrea and Pippow, Andreas and Cambon-Thomsen, Anne and Sedani, Ashni and Goble, Carole and Evelo, Chris and Kee Ong, Chuang and Wood, Colin and Pommier, Cyril and J. B. Clarke, Daniel and Welter, Danielle and Henderson, David and Batista, Dominique and Reilly, Dorothy and Alharbi, Ebtisam and van der Horst, Eelke and Willighagen, Egon and Reynares, Emiliano and Vos, Emma and LeFloch, Erwan and Marin del Pico, Eva and Ronzano, Francesco and Kroh, Franziska and Xu, Fuqi and Backianathan, Gabriel and Papadotas, George and Witt, Gesa and Hurst, Hannah and Van Vlijmen, Herman and Emam, Ibrahim and Liyanage, Isuru and Neefs, Jean-Marc and Strubel, Jolanda and Quast, Karsten and van Bochove, Kees and Dauth, Kurt and Furlong, Laura and Garcia, Leyla and Giovanni, Lucas and Kohler, Manfred and Pruess, Manuela and Ibberson, Mark and Cook, Martin and Courtot, Melanie and d’Arcy, Mike and Juty, Nick and Lynch, Nick and Engkvist, Ola and Deniz Beyan, Oya and Peeters, Paul and Woollard, Peter and Papadopoulos, Petros and Gribbon, Philip and Sahay, Ratnesh and Giessmann, Robert and Verbeeck, Rudi and Capella Gutierrez, Salvador and Lusher, Scott and Beier, Sebastian and Singh, Sukhi and Sansone, Susanna-Assunta and Plasterer, Tom and Burdett, Tony and Abbassi-Daloii, Tooba and Goldmann, Ulrich and Grouès, Valentin and Ioannidis, Vassilios and P. Satagopam, Venkata and Sedlyarov, Vitaly and Gu, Wei and Gaidya, Yojana and Warnes, Zachary
   software. apr, 2022
   

   @software{Rocca-Serra_The_FAIR_Cookbook_2022,
     author = {Rocca-Serra, Philippe and J G Gray, Alasdair and Delfin Rossaro, Alejandra and Splendiani, Andrea and Zaliani, Andrea and Pippow, Andreas and Cambon-Thomsen, Anne and Sedani, Ashni and Goble, Carole and Evelo, Chris and Kee Ong, Chuang and Wood, Colin and Pommier, Cyril and J. B. Clarke, Daniel and Welter, Danielle and Henderson, David and Batista, Dominique and Reilly, Dorothy and Alharbi, Ebtisam and van der Horst, Eelke and Willighagen, Egon and Reynares, Emiliano and Vos, Emma and LeFloch, Erwan and Marin del Pico, Eva and Ronzano, Francesco and Kroh, Franziska and Xu, Fuqi and Backianathan, Gabriel and Papadotas, George and Witt, Gesa and Hurst, Hannah and Van Vlijmen, Herman and Emam, Ibrahim and Liyanage, Isuru and Neefs, Jean-Marc and Strubel, Jolanda and Quast, Karsten and van Bochove, Kees and Dauth, Kurt and Furlong, Laura and Garcia, Leyla and Giovanni, Lucas and Kohler, Manfred and Pruess, Manuela and Ibberson, Mark and Cook, Martin and Courtot, Melanie and d'Arcy, Mike and Juty, Nick and Lynch, Nick and Engkvist, Ola and Deniz Beyan, Oya and Peeters, Paul and Woollard, Peter and Papadopoulos, Petros and Gribbon, Philip and Sahay, Ratnesh and Giessmann, Robert and Verbeeck, Rudi and Capella Gutierrez, Salvador and Lusher, Scott and Beier, Sebastian and Singh, Sukhi and Sansone, Susanna-Assunta and Plasterer, Tom and Burdett, Tony and Abbassi-Daloii, Tooba and Goldmann, Ulrich and Grouès, Valentin and Ioannidis, Vassilios and P. Satagopam, Venkata and Sedlyarov, Vitaly and Gu, Wei and Gaidya, Yojana and Warnes, Zachary},
     license = {CC-BY-4.0},
     month = apr,
     title = {{The FAIR Cookbook}},
     url = {https://github.com/FAIRplus/the-fair-cookbook/},
     version = {0.1.0},
     year = {2022}
   }
   
5. Bioschemas data harvesting project report
   Gray, Alasdair J G and Papadopoulos, Petros and Gaignard, Alban and Rosnet, Thomas and Mičetić, Ivan
   Technical Report. BioHackrXiv. mar, 2022
   

   The promise of Bioschemas is that it makes consuming data from multiple resources more straightforward. However, this hypothesis has not been tested by conducting a large scale harvest of deployed markup and making this available for others to reuse. Therefore, the goal of this hackathon project is to harvest a collection of Bioschemas markup from a number of different sites listed on the Bioschemas live deploys page using the Bioschemas Markup Scraper and Extractor (BMUSE). The harvested data will be made available for others and loaded into a triplestore to allow for further exploration.

   @techreport{gray:bioschemas-harvesting:2022,
     title = {Bioschemas data harvesting project report},
     url = {https://biohackrxiv.org/y6gbq/},
     doi = {10.37044/osf.io/y6gbq},
     publisher = {BioHackrXiv},
     author = {Gray, Alasdair J G and Papadopoulos, Petros and Gaignard, Alban and Rosnet, Thomas and Mičetić, Ivan},
     year = {2022},
     month = mar
   }
   
6. Creating and Exploiting the Intrinsically Disordered Protein Knowledge Graph (IDP-KG)
   Gray, Alasdair J. G. and Papadopoulos, Petros and Asif, Imran and Micetic, Ivan and Hatos, András
   In 13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, SWAT4HCLS 2022, Virtual Event, Leiden, The Netherlands, January 10th to 14th, 2022, CEUR Workshop Proceedings, 3127, pages 1–10, CEUR-WS.org, 2022
   

   There are many data sources containing overlapping information about Intrinsically Disordered Proteins (IDP). IDPcentral aims to be a registry to aid the discovery of data about proteins known to be intrinsically disordered by aggregating the content from these sources. Traditional ETL approaches for populating IDPcentral require the API and data model of each source to be wrapped and then transformed into a common model. In this paper, we investigate using Bioschemas markup as a mechanism to populate the IDPcentral registry by constructing the Intrinsically Disordered Protein Knowledge Graph (IDP-KG). Bioschemas markup is a machine-readable, lightweight representation of the content of each page in the site that is embedded in the HTML. For any site it is accessible through a HTTP request. We harvest the Bioschemas markup in three IDP sources and show the resulting IDP-KG has the same breadth of proteins available as the original sources, and can be used to gain deeper insight into their content by querying them as a single, consolidated knowledge graph.

   @inproceedings{GrayEtal:bioschemas-idpkg:swat4hcls2022,
     author = {Gray, Alasdair J. G. and Papadopoulos, Petros and Asif, Imran and Micetic, Ivan and Hatos, Andr{\'{a}}s},
     title = {Creating and Exploiting the Intrinsically Disordered Protein Knowledge Graph {(IDP-KG)}},
     booktitle = {13th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, {SWAT4HCLS} 2022, Virtual Event, Leiden, The Netherlands, January 10th to 14th, 2022},
     series = {{CEUR} Workshop Proceedings},
     volume = {3127},
     pages = {1--10},
     publisher = {CEUR-WS.org},
     year = {2022},
     url = {http://ceur-ws.org/Vol-3127/paper-1.pdf}
   }
   

2021

1. Reference Statistics in Wikidata Topical Subsets
   Hosseini Beghaeiraveri, Seyed Amir and Gray, Alasdair J. G. and McNeill, Fiona
   In Proceedings of the 2nd Wikidata Workshop (Wikidata 2021), co-located with the 20th International Semantic Web Conference (ISWC 2021), 2021
   

   Wikidata is the only general-purpose open knowledge graph with the capability of specifying references for every single statement. Currently, about 68% of Wikidata statements have at least one reference but the quality of these references is rarely covered in data quality studies. There is also a lack of a comprehensive framework for evaluating references. In this paper, we investigate the statistics of Wikidata references in 6 topical subsets of Wikidata. We compare these statistics over two Wikidata dumps; one from 2016 and one from 2021.

   @inproceedings{HosseiniBeghaeiraveri2021:RefStats:wikidata2021,
     title = {Reference Statistics in Wikidata Topical Subsets},
     booktitle = {Proceedings of the 2nd Wikidata Workshop (Wikidata 2021), co-located with the 20th International Semantic Web Conference (ISWC 2021)},
     keywords = {Reference quality, Wikidata, Data quality, Topical subset, WikiProject, Gene Wiki},
     author = {Hosseini Beghaeiraveri, Seyed Amir and Gray, Alasdair J. G. and McNeill, Fiona},
     year = {2021},
     month = oct,
     url = {http://ceur-ws.org/Vol-2982/paper-3.pdf}
   }
   
2. Experiences of Using WDumper to Create Topical Subsets from Wikidata
   Hosseini Beghaeiraveri, Seyed Amir and Gray, Alasdair J. G. and McNeill, Fiona
   In Proceedings of the 2nd International Workshop on Knowledge Graph Construction, co-located with the 18th Extended Semantic Web Conference (ESWC 2021), CEUR Workshop Proceedings, 2873, CEUR Workshop Proceedings (CEUR-WS.org), 2021
   

   Wikidata is a general-purpose knowledge graph covering a wide variety of topics with content being crowd-sourced through an open wiki. There are now over 90M interrelated data items in Wikidata which are accessible through a public query endpoint and data dumps. However, execution timeout limits and the size of data dumps make it difficult to use the data. The creation of arbitrary topical subsets of Wikidata, where only the relevant data is kept, would enable reuse of that data with the benefits of cost reduction, ease of access, and flexibility. In this paper, we provide a formal definition of topical subsets over the Wikidata Knowledge Graph and evaluate a third-party tool (WDumper) to extract these topical subsets from Wikidata.

   @inproceedings{HosseiniBeghaeiraveri2021:TopicalSubsets:KGConstruction2021,
     title = {Experiences of Using WDumper to Create Topical Subsets from Wikidata},
     booktitle = {Proceedings of the 2nd International Workshop on Knowledge Graph Construction, co-located with the 18th Extended Semantic Web Conference (ESWC 2021)},
     keywords = {Wikidata, Topical subset, WikiProject, Gene Wiki},
     author = {{Hosseini Beghaeiraveri}, {Seyed Amir} and Gray, {Alasdair J. G.} and McNeill, Fiona},
     year = {2021},
     month = jun,
     series = {CEUR Workshop Proceedings},
     publisher = {CEUR Workshop Proceedings (CEUR-WS.org)},
     volume = {2873},
     url = {http://ceur-ws.org/Vol-2873/paper13.pdf}
   }
   
3. Exploiting Bioschemas Markup to Populate IDPcentral
   Gray, Alasdair J G and Papadopoulos, Petros and Mičetić, Ivan and Hatos, András
   Technical Report. BioHackrXiv. jun, 2021
   

   One of the goals of the ELIXIR Intrinsically Disordered Protein (IDP) community is create a registry called IDPcentral. The registry will aggregate data contained in the community’s specialist data sources such as DisProt, MobiDB, and Protein Ensemble Database (PED) so that proteins that are known to be intrinsically disordered can be discovered; with summary details of the protein presented, and the specialist source consulted for more detailed data. At the ELIXIR BioHackathon-Europe 2020, we aimed to investigate the feasibility of populating IDPcentral harvesting the Bioschemas markup that has been deployed on the IDP community data sources. The benefit of using Bioschemas markup, which is embedded in the HTML web pages for each protein in the data source, is that a standard harvesting approach can be used for all data sources; rather than needing bespoke wrappers for each data source API. We expect to harvest the markup using the Bioschemas Markup Scraper and Extractor (BMUSE) tool that has been developed specifically for this purpose. The challenge, however, is that the sources contain overlapping information about proteins but use different identifiers for the proteins. After the data has been harvested, it will need to be processed so that information about a particular protein, which will come from multiple sources, is consolidated into a single concept for the protein, with links back to where each piece of data originated. As well as populating the IDPcentral registry, we plan to consolidate the markup into a knowledge graph that can be queried to gain further insight into the IDPs.

   @techreport{gray:bioschemas-idpcntral:2021,
     title = {Exploiting Bioschemas Markup to Populate IDPcentral},
     url = {https://biohackrxiv.org/v3jct},
     doi = {10.37044/osf.io/v3jct},
     publisher = {BioHackrXiv},
     author = {Gray, Alasdair J G and Papadopoulos, Petros and Mičetić, Ivan and Hatos, András},
     year = {2021},
     month = jun
   }
   
4. Knowledge graphs and wikidata subsetting
   Labra-Gayo, Jose E and Hevia, Alejandro G and Álvarez, Daniel F and Ammar, Ammar and Brickley, Dan and Gray, Alasdair J G and Prud’hommeaux, Eric and Slenter, Denise and Solbrig, Harold and Beghaeiraveri, Seyed A H and et al.
   Technical Report. BioHackrXiv. apr, 2021
   

   Knowledge graphs have successfully been adopted by academia, governement and industry to represent large scale knowledge bases. Open and collaborative knowledge graphs such as Wikidata capture knowledge from different domains and harmonize them under a common format, making it easier for researchers to access the data while also supporting Open Science. Wikidata keeps getting bigger and better, which subsumes integration use cases. Having a large amount of data such as the one presented in a scopeless Wikidata offers some advantages, e.g., unique access point and common format, but also poses some challenges, e.g., performance. Regular wikidata users are not unfamiliar with running into frequent timeouts of submitted queries. Due to its popularity, limits have been imposed to allow for fair access to many. However this suppreses many interesting and complex queries that require more computational power and resources. Replicating Wikidata on one’s own infrastructure can be a solution which also offers a snapshot of the contents of wikidata at some given point in time. There is no need to replicate Wikidata in full, it is possible to work with subsets targeting, for instance, a particular domain. Creating those subsets has emerged as an alternative to reduce the amount and spectrum of data offered by Wikidata. Less data makes more complex queries possible while still keeping the compatibility with the whole Wikidata as the model is kept. In this paper we report the tasks done as part of a Wikidata subsetting project during the Virtual BioHackathon Europe 2020 and SWAT4(HC)LS 2021, which had already started at NBDC/DBCLS BioHackathon 2019 in Japan, SWAT4(HC)LS hackathon 2019, and Virtual COVID-19 BioHackathon 2019. We describe some of approaches we identified to create subsets and some susbsets from the Life Sciences domain as well as other use cases we also discussed.

   @techreport{labra-gayo:kg-subsetting:biohackrxiv2021,
     title = {Knowledge graphs and wikidata subsetting},
     url = {https://biohackrxiv.org/wu9et},
     doi = {10.37044/osf.io/wu9et},
     publisher = {BioHackrXiv},
     author = {Labra-Gayo, Jose E and Hevia, Alejandro G and Álvarez, Daniel F and Ammar, Ammar and Brickley, Dan and Gray, Alasdair J G and Prud'hommeaux, Eric and Slenter, Denise and Solbrig, Harold and Beghaeiraveri, Seyed A H and et al.},
     year = {2021},
     month = apr
   }
   
5. RO-Crate Metadata Specification 1.1.1
   Sefton, Peter and Carragáin, Eoghan Ó and Soiland-Reyes, Stian and Corcho, Oscar and Garijo, Daniel and Palma, Raul and Coppens, Frederik and Goble, Carole and Fernández, José María and Chard, Kyle and Gomez-Perez, Jose Manuel and Crusoe, Michael R and Eguinoa, Ignacio and Juty, Nick and Holmes, Kristi and Clark, Jason A. and Capella-Gutierrez, Salvador and Gray, Alasdair J. G. and Owen, Stuart and Williams, Alan R. and Tartari, Giacomo and Bacall, Finn and Thelen, Thomas and Ménager, Hervé and Rodríguez-Navas, Laura and Walk, Paul and brandon whitehead and Wilkinson, Mark and Groth, Paul and Bremer, Erich and Castro, LJ Garcia and Sebby, Karl and Kanitz, Alexander and Trisovic, Ana and Kennedy, Gavin and Graves, Mark and Koehorst, Jasper and Leo, Simone and Portier, Marc
   Technical Report. researchobject.org. feb, 2021
   Recommendation published by researchobject.org - see https://w3id.org/ro/crate/1.1 for web version.
   

   This document specifies a method, known as RO-Crate (Research Object Crate), of aggregating and describing research data with associated metadata. RO-Crates can aggregate and describe any resource including files, URI-addressable resources, or use other addressing schemes to locate digital or physical data. RO-Crates can describe data in aggregate and at the individual resource level, with metadata to aid in discovery, re-use and long term management of data. Metadata includes the ability to describe the context of data and the entities involved in its production, use and reuse. For example: who created it, using which equipment, software and workflows, under what licenses can it be re-used, where was it collected, and/or where is it about.RO-Crate uses JSON-LD to to express this metadata using linked data, describing data resources as well as contextual entities such as people, organizations, software and equipment as a series of linked JSON-LD objects - using common published vocabularies, chiefly schema.org.The core of RO-Crate is a JSON-LD file, the RO-Crate Metadata File, named ro-crate-metadata.json. This file contains structured metadata about the dataset as a whole (the Root Data Entity) and, optionally, about some or all of its files. This provides a simple way to, for example, assert the authors (e.g. people, organizations) of the RO-Crate or one its files, or to capture more complex provenance for files, such as how they were created using software and equipment.While providing the formal specification for RO-Crate, this document also aims to be a practical guide for software authors to create tools for generating and consuming research data packages, with explanation by examples.

   @techreport{RO-Crate-1-1,
     title = {RO-Crate Metadata Specification 1.1.1},
     author = {Sefton, Peter and Carrag{\'a}in, {Eoghan {\'O}} and Soiland-Reyes, Stian and Corcho, Oscar and Garijo, Daniel and Palma, Raul and Coppens, Frederik and Goble, Carole and Fern{\'a}ndez, {Jos{\'e} Mar{\'i}a} and Chard, Kyle and Gomez-Perez, {Jose Manuel} and Crusoe, {Michael R} and Eguinoa, Ignacio and Juty, Nick and Holmes, Kristi and Clark, {Jason A.} and Capella-Gutierrez, Salvador and Gray, {Alasdair J. G.} and Owen, Stuart and Williams, {Alan R.} and Tartari, Giacomo and Bacall, Finn and Thelen, Thomas and M{\'e}nager, Herv{\'e} and Rodr{\'i}guez-Navas, Laura and Walk, Paul and brandon whitehead and Wilkinson, Mark and Groth, Paul and Bremer, Erich and Castro, {LJ Garcia} and Sebby, Karl and Kanitz, Alexander and Trisovic, Ana and Kennedy, Gavin and Graves, Mark and Koehorst, Jasper and Leo, Simone and Portier, Marc},
     note = {Recommendation published by researchobject.org - see https://w3id.org/ro/crate/1.1 for web version.},
     year = {2021},
     month = feb,
     doi = {10.5281/zenodo.4541002},
     publisher = {researchobject.org},
     address = {United Kingdom}
   }
   
6. SPaR.txt, a cheap Shallow Parsing approach for Regulatory texts
   Kruiper, Ruben and Konstas, Ioannis and Gray, Alasdair J G and Sadeghineko, Fahrad and Watson, Richard and Kumar, Bimal
   In Natural Legal Language Processing workshop, EMNLP, Punta Cana, Dominican Republic, pages 129-143, Association for Computational Linguistics, 2021
   

   Automated Compliance Checking (ACC) systems aim to semantically parse building regulations to a set of rules. However, semantic parsing is known to be hard and requires large amounts of training data. The complexity of creating such training data has led to research that focuses on small sub-tasks, such as shallow parsing or the extraction of a limited subset of rules. This study introduces a shallow parsing task for which training data is relatively cheap to create, with the aim of learning a lexicon for ACC. We annotate a small domain-specific dataset of 200 sentences, SPaR.txt, and train a sequence tagger that achieves 79,93 F1-score on the test set. We then show through manual evaluation that the model identifies most (89,84%) defined terms in a set of building regulation documents, and that both contiguous and discontiguous Multi-Word Expressions (MWE) are discovered with reasonable accuracy (70,3%).

   @inproceedings{Kruiper2021:SPaRtxt:nllp2021,
     author = {Kruiper, Ruben and Konstas, Ioannis and Gray, Alasdair J G and Sadeghineko, Fahrad and Watson, Richard and Kumar, Bimal},
     title = {SPaR.txt, a cheap Shallow Parsing approach for Regulatory texts},
     optcrossref = {},
     optkey = {},
     booktitle = {Natural Legal Language Processing workshop, EMNLP},
     year = {2021},
     opteditor = {},
     optvolume = {},
     optnumber = {},
     optseries = {},
     pages = {129-143},
     optmonth = nov,
     address = {Punta Cana, Dominican Republic},
     optorganization = {},
     publisher = {Association for Computational Linguistics},
     optnote = {},
     url = {https://aclanthology.org/2021.nllp-1.14},
     optannote = {}
   }
   
7. A Novel Method That Identifies The Hidden Properties Of A Person’s Name In Kanji Or Hanzi
   Zhao, Hua and Kamareddine, Fairouz and Gray, Alasdair J G and Zantout, Hind
   In The 8th Multidisciplinary International Social Networks Conference, New York, NY, USA, MISNC2021, pages 79–85, Association for Computing Machinery, 2021
   

   Most Japanese persons’ Kanji names have similar characters with ’Hanzi’. For example, ’吉田悠人’ and ’欧阳沛南’ are two persons’ names. ’吉田悠人’ is a Kanji name, ’欧阳沛南’ is a Hanzi name. It is a challenge for a computer to identify the name origins between ’Hanzi’ and ’Kanji’ of a person’s name. In addition, we found that there are limited existing methods to identify more than one hidden property of people’s names at one time. In this paper, we aim to build a method that can identify the hidden properties of Hanzi names and Kanji names. Our novel method can point out the origin, the surname and the given name of a person’s name. The evaluation result shows that our method is better than an existing system ’TextBlob’ on predicting the origins of people’s names. The accuracy of our proposed method is 86.87%.

   @inproceedings{Hua:properties-name:MISNC2021,
     author = {Zhao, Hua and Kamareddine, Fairouz and Gray, Alasdair J G and Zantout, Hind},
     title = {A Novel Method That Identifies The Hidden Properties Of A Person’s Name In Kanji Or Hanzi},
     year = {2021},
     isbn = {9781450396011},
     publisher = {Association for Computing Machinery},
     address = {New York, NY, USA},
     doi = {10.1145/3504006.3504022},
     booktitle = {The 8th Multidisciplinary International Social Networks Conference},
     pages = {79–85},
     numpages = {7},
     keywords = {Text Diversity, Name Identification, Machine Learning, Hidden property},
     location = {Bergen, Norway},
     series = {MISNC2021}
   }
   
8. Using Nanopublications to Detect and Explain Contradictory Research Claims
   Asif, Imran and Tiddi, Ilaria and Gray, Alasdair J. G.
   In 2021 IEEE 17th International Conference on eScience (eScience), pages 1-10, 2021
   

   We tackle the problem of automatically detecting conflicting claims in research outputs. This has become even more urgent in recent years, with the increasing volume of scientific publications available. Researchers are struggling to keep pace with the literature, and to efficiently make comparisons between the results of different published studies. We hypothesise that the difficult and time-consuming process of searching and comparing results across research publications can be facilitated using machine-readable, standardised knowledge representation methods. To this end, we propose to exploit Nanopublications as the standard framework to represent the claims in research studies, and use provenance data expressed by the model as an indicator of the source of the contradiction between different claims. We evaluate this idea over the Cooperation Databank (CoDa); a repository of social science studies. Our results show that the use of provenance information can be a good factor to identify the cause of conflicting claims, and that our method can support scientists in comparing literature in a more automated way.

   @inproceedings{asif:nanopub-contradictions:eScience2021,
     author = {Asif, Imran and Tiddi, Ilaria and Gray, Alasdair J. G.},
     booktitle = {2021 IEEE 17th International Conference on eScience (eScience)},
     title = {Using Nanopublications to Detect and Explain Contradictory Research Claims},
     year = {2021},
     pages = {1-10},
     doi = {10.1109/eScience51609.2021.00010}
   }
   

2020

1. Data integration for offshore decommissioning waste management
   Akinyemi, Abiodun G. and Sun, Ming and Gray, Alasdair J. G.
   Automation in Construction, 109:103010, Elsevier, 2020
   

   Offshore decommissioning represents significant business opportunities for oil and gas service companies. However, for owners of offshore assets and regulators, it is a liability because of the associated costs. One way of mitigating decommissioning costs is through the sales and reuse of decommissioned items. To achieve this effectively, reliability assessment of decommissioned items is required. Such an assessment relies on data collected on the various items over the lifecycle of an engineering asset. Considering that offshore platforms have a design life of about 25 years and data management techniques and tools are constantly evolving, data captured about items to be decommissioned will be in varying forms. In addition, considering the many stakeholders involved with a facility over its lifecycle, information representation of the items will have variations. These challenges make data integration difficult. As a result, this research developed a data integration framework that makes use of Semantic Web technologies and ISO 15926 - a standard for process plant data integration - for rapid assessment of decommissioned items. The proposed solution helps in determining the reuse potential of decommissioned items, which can save on cost and benefit the environment.

   @article{Akinyemi:offshore-data-integration:2020,
     doi = {10.1016/j.autcon.2019.103010},
     url = {https://www.sciencedirect.com/science/article/pii/S0926580518304059},
     year = {2020},
     month = nov,
     publisher = {Elsevier},
     volume = {109},
     pages = {103010},
     author = {Akinyemi, Abiodun G. and Sun, Ming and Gray, Alasdair J. G.},
     title = {Data integration for offshore decommissioning waste management},
     journal = {Automation in Construction}
   }
   

2019

1. Generating corrupted data sources for the evaluation of matching systems
   McNeill, Fiona and Bental, Diana and Gray, Alasdair J. G. and Jedrzejczyk, Sabina and Alsadeeqi, Ahmad
   In The Fourteenth International Workshop on Ontology Matching, CEUR Workshop Proceedings, 2536, pages 41–45, CEUR Workshop Proceedings (CEUR-WS.org), 2019
   

   One of the most difficult aspects of developing matching systems – whether for matching ontologies or for other types of mismatched data – is evaluation. The accuracy of matchers are usually evaluated by measuring the results produced by the systems against reference sets, but gold-standard reference sets are expensive and difficult to create. In this paper we introduce crptr, which generates multiple variations of different sorts of dataset, where the degree of variation is controlled, in order that they can be used to evaluate matchers in different context.

   @inproceedings{McNeill:crptr-matching-evaluation:OM2019,
     title = {Generating corrupted data sources for the evaluation of matching systems},
     keywords = {Matching, Evaluation, Data Corruption},
     author = {McNeill, Fiona and Bental, Diana and Gray, Alasdair J. G. and Jedrzejczyk, Sabina and Alsadeeqi, Ahmad},
     year = {2019},
     month = oct,
     series = {CEUR Workshop Proceedings},
     publisher = {CEUR Workshop Proceedings (CEUR-WS.org)},
     volume = {2536},
     pages = {41--45},
     booktitle = {The Fourteenth International Workshop on Ontology Matching},
     url = {http://ceur-ws.org/Vol-2536/om2019_STpaper2.pdf}
   }
   
2. Data Quality Issues in Current Nanopublications
   Asif, Imran and Chen-Burger, Jessica and Gray, Alasdair J. G.
   In 2019 15th International Conference on eScience (eScience), , pages 522-527, 2019
   

   Nanopublications are a granular way of publishing scientific claims together with their associated provenance and publication information. More than 10 million nanopublications have been published by a handful of researchers covering a wide range of topics within the life sciences. We were motivated to replicate an existing analysis of these nanopublications, but then went deeper into the structure of the existing nanopublications. In this paper, we analyse the usage of nanopublications by investigating the distribution of triples in each part and discuss the data quality issues that were subsequently revealed. We argue that there is a need for the community to develop a set of guidelines for the modelling of nanopublications.

   @inproceedings{Asif:NanopubQuality:eScience2019,
     author = {Asif, Imran and Chen-Burger, Jessica and Gray, Alasdair J. G.},
     booktitle = {2019 15th International Conference on eScience (eScience)},
     title = {Data Quality Issues in Current Nanopublications},
     year = {2019},
     volume = {},
     number = {},
     pages = {522-527},
     keywords = {},
     doi = {10.1109/eScience.2019.00069},
     month = sep
   }
   
3. The Semantic Web - 16th International Conference, ESWC 2019, Portorož, Slovenia, June 2-6, 2019, Proceedings
   Hitzler, Pascal and Fernández, Miriam and Janowicz, Krzysztof and Zaveri, Amrapali and Gray, Alasdair J. G. and López, Vanessa and Haller, Armin and Hammar, Karl
   Lecture Notes in Computer Science, 11503, Springer, 2019
   ISBN: 978-3-030-21347-3
   

   This book constitutes the refereed proceedings of the 16th International Semantic Web Conference, ESWC 2019, held in Portorož, Slovenia. The 39 revised full papers presented were carefully reviewed and selected from 134 submissions. The papers are organized in three tracks: research track, resources track, and in-use track and deal with the following topical areas: distribution and decentralisation, velocity on the Web, research of research, ontologies and reasoning, linked data, natural language processing and information retrieval, semantic data management and data infrastructures, social and human aspects of the Semantic Web, and, machine learning.

   @proceedings{eswc2019,
     editor = {Hitzler, Pascal and Fern{\'{a}}ndez, Miriam and Janowicz, Krzysztof and Zaveri, Amrapali and Gray, Alasdair J. G. and L{\'{o}}pez, Vanessa and Haller, Armin and Hammar, Karl},
     title = {The Semantic Web - 16th International Conference, {ESWC} 2019, Portoro{\v{z}},
                    Slovenia, June 2-6, 2019, Proceedings},
     series = {Lecture Notes in Computer Science},
     volume = {11503},
     publisher = {Springer},
     month = jun,
     year = {2019},
     url = {https://doi.org/10.1007/978-3-030-21348-0},
     doi = {10.1007/978-3-030-21348-0},
     isbn = {978-3-030-21347-3}
   }
   
4. ToCo: An Ontology for Representing Hybrid Telecommunication Networks
   Zhou, Qianru and Gray, Alasdair J. G. and McLaughlin, Stephen
   In The Semantic Web - 16th International Conference, ESWC 2019, Portorož, Slovenia, June 2-6, 2019, Proceedings, Lecture Notes in Computer Science, 11503, pages 507–522, Springer, 2019
   

   The TOUCAN project proposed an ontology for telecommunication networks with hybrid technologies – the TOUCAN Ontology (ToCo), available at http://purl.org/toco/, as well as a knowledge design pattern Device-Interface-Link (DIL) pattern. The core classes and relationships forming the ontology are discussed in detail. The ToCo ontology can describe the physical infrastructure, quality of channel, services and users in heterogeneous telecommunication networks which span multiple technology domains. The DIL pattern is observed and summarised when modelling networks with various technology domains. Examples and use cases of ToCo are presented for demonstration.

   @inproceedings{DBLP:conf/esws/ZhouGM19,
     author = {Zhou, Qianru and Gray, Alasdair J. G. and McLaughlin, Stephen},
     title = {ToCo: An Ontology for Representing Hybrid Telecommunication Networks},
     booktitle = {The Semantic Web - 16th International Conference, {ESWC} 2019, Portoro{\v{z}},
                    Slovenia, June 2-6, 2019, Proceedings},
     series = {Lecture Notes in Computer Science},
     volume = {11503},
     pages = {507--522},
     publisher = {Springer},
     month = jun,
     year = {2019},
     url = {https://doi.org/10.1007/978-3-030-21348-0\_33},
     doi = {10.1007/978-3-030-21348-0\_33}
   }
   
5. SARA - A Semantic Access Point Resource Allocation Service for Heterogenous Wireless Networks
   Zhou, Qianru and Gray, Alasdair J. G. and Pezaros, Dimitrios and McLaughlin, Stephen
   In 2019 Wireless Days, WD 2019, Manchester, United Kingdom, April 24-26, 2019, pages 1–8, IEEE, 2019
   

   In this paper, we present SARA, a Semantic Access point Resource Allocation service for heterogenous wireless networks with various wireless access technologies existing together. By automatically reasoning on the knowledge base of the full system provided by a knowledge based autonomic network management system - SEANET, SARA selects the access point providing the best quality of service among the different access technologies. Based on an ontology assisted knowledge based system SEANET, SARA can also adapt the access point selection strategy according to customer defined rules automatically. Results of our evaluation based on emulated networks with hybrid access technologies and various scales show that SARA is able to improve the channel condition, in terms of throughput, evidently. Comparisons with current AP selection algorithms demonstrate that SARA outperforms the existing AP selection algorithms. The overhead in terms of time expense is reasonable and is shown to be faster than traditional access point selection approaches.

   @inproceedings{DBLP:conf/wd/ZhouGPM19,
     author = {Zhou, Qianru and Gray, Alasdair J. G. and Pezaros, Dimitrios and McLaughlin, Stephen},
     title = {{SARA} - {A} Semantic Access Point Resource Allocation Service for
                    Heterogenous Wireless Networks},
     booktitle = {2019 Wireless Days, {WD} 2019, Manchester, United Kingdom, April 24-26,
                    2019},
     pages = {1--8},
     publisher = {{IEEE}},
     month = apr,
     year = {2019},
     url = {https://doi.org/10.1109/WD.2019.8734260},
     doi = {10.1109/WD.2019.8734260}
   }
   

2018

1. Using a Jupyter Notebook to perform a reproducible scientific analysis over semantic web sources
   Gray, Alasdair J G
   In Enabling Open Semantic Science, Monterey, California, USA, 2018
   Executable version: https://mybinder.org/v2/gh/AlasdairGray/SemSci2018/master?filepath=SemSci2018%20Publication.ipynb
   

   In recent years there has been a reproducibility crisis in science. Computational notebooks, such as Jupyter, have been touted as one solution to this problem. However, when executing analyses over live SPARQL endpoints, we get different answers depending upon when the analysis in the notebook was executed. In this paper, we identify some of the issues discovered in trying to develop a reproducible analysis over a collection of biomedical data sources and suggest some best practice to overcome these issues.

   @inproceedings{Gray2018:jupyter:SemSci2018,
     author = {Gray, Alasdair J G},
     title = {Using a Jupyter Notebook to perform a reproducible scientific analysis over semantic web sources},
     optcrossref = {},
     optkey = {},
     booktitle = {Enabling Open Semantic Science},
     year = {2018},
     opteditor = {},
     optvolume = {},
     optnumber = {},
     optseries = {},
     optpages = {},
     month = oct,
     address = {Monterey, California, USA},
     optorganization = {},
     optpublisher = {},
     note = {Executable version: https://mybinder.org/v2/gh/AlasdairGray/SemSci2018/master?filepath=SemSci2018%20Publication.ipynb},
     url = {http://ceur-ws.org/Vol-2184/paper-02/paper-02.html},
     optannote = {}
   }
   
2. An ontology-based data integration framework for construction information management
   Akinyemi, Abiodun and Sun, Ming and Gray, Alasdair J G
   Proceedings of the Institution of Civil Engineers - Management, Procurement and Law, 171(3):111–125, Thomas Telford Ltd., 2018
   

   Information management during the construction phase of a built asset involves multiple stakeholders using multiple software applications to generate and store data. This is problematic as data come in different forms and are labour intensive to piece together. Existing solutions to this problem are predominantly in proprietary applications, which are sometimes cost prohibitive for small engineering firms, or conceptual studies with use cases that cannot be easily adapted. In view of these limitations, this research presents an ontology-based data integration framework that makes use of open-source tools that support Semantic Web technologies. The proposed framework enables rapid answering of queries over construction data integrated from heterogeneous sources, data quality checks and reuse of project software resources. The attributes and functionalities of the proposed solution align with the requirements common to small firms with limited information technology skill and budget. Consequently, this solution can be of great benefit for their data projects.

   @article{Akinyemi_2018,
     doi = {10.1680/jmapl.17.00052},
     url = {https://doi.org/10.1680%2Fjmapl.17.00052},
     year = {2018},
     month = jun,
     publisher = {Thomas Telford Ltd.},
     volume = {171},
     number = {3},
     pages = {111--125},
     author = {Akinyemi, Abiodun and Sun, Ming and Gray, Alasdair J G},
     title = {An ontology-based data integration framework for construction information management},
     journal = {Proceedings of the Institution of Civil Engineers - Management, Procurement and Law}
   }
   
3. ReasoNet: Inferring Network Policies Using Ontologies
   Rotsos, Charalampos and Farshad, Arsham and King, Daniel and Hutchison, David and Zhou, Qianru and Gray, Alasdair J. G. and Wang, Cheng-Xiang and McLaughlin, Stephen
   In 4th IEEE Conference on Network Softwarization and Workshops, NetSoft 2018, Montreal, QC, Canada, June 25-29, 2018, pages 159–167, IEEE, 2018
   

   Modern Software Defined Networking (SDN) control stacks consist of multiple abstraction and virtualization layers to enable flexibility in the development of new control features. Rich data modeling frameworks are essential when sharing information across control layers. Unfortunately, existing Network Operating System (NOS) data modeling capabilities are limited to simple type-checking and code templating. We present an exploration of a more extreme point on SDN data modeling: ReasoNet. Developers can use semantic web technologies to enrich their data models with reasoning rules and integrity/consistency constraints, and automate state inference across layers. We demonstrate the ability of ReasoNet to automate state verification and cross-layer debugging, through the implementation of two popular control applications, a learning switch and a Quality of Service (QoS) policy engine.

   @inproceedings{DBLP:conf/netsoft/RotsosFKHZGWM18,
     author = {Rotsos, Charalampos and Farshad, Arsham and King, Daniel and Hutchison, David and Zhou, Qianru and Gray, Alasdair J. G. and Wang, Cheng{-}Xiang and McLaughlin, Stephen},
     title = {ReasoNet: Inferring Network Policies Using Ontologies},
     booktitle = {4th {IEEE} Conference on Network Softwarization and Workshops, NetSoft
                    2018, Montreal, QC, Canada, June 25-29, 2018},
     pages = {159--167},
     publisher = {{IEEE}},
     month = jun,
     year = {2018},
     url = {https://doi.org/10.1109/NETSOFT.2018.8460050},
     doi = {10.1109/NETSOFT.2018.8460050}
   }
   
4. The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY
   Harding, Simon D. and Sharman, Joanna L. and Faccenda, Elena and Southan, Christopher and Pawson, Adam J. and Ireland, Sam and Gray, Alasdair J. G. and Bruce, Liam and Alexander, Stephen P. H. and Anderton, Stephen and Bryant, Clare and Davenport, Anthony P. and Doerig, Christian and Fabbro, Doriano and Levi-Schaffer, Francesca and Spedding, Michael and Davies, Jamie A. and Nc-Iuphar
   Nucleic Acids Research, 46(Database-Issue):D1091–D1106, 2018
   

   The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org) and its precursor IUPHAR-DB, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). As previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015. Our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. As an important addition, we also introduce our newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org). This has been ‘forked’ from the well-established GtoPdb data model and expanded into new types of data related to the immune system and inflammatory processes. This includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new IUPHAR expert committees. Designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.

   @article{Harding:GtoPdb:NAR2018,
     author = {Harding, Simon D. and Sharman, Joanna L. and Faccenda, Elena and Southan, Christopher and Pawson, Adam J. and Ireland, Sam and Gray, Alasdair J. G. and Bruce, Liam and Alexander, Stephen P. H. and Anderton, Stephen and Bryant, Clare and Davenport, Anthony P. and Doerig, Christian and Fabbro, Doriano and Levi{-}Schaffer, Francesca and Spedding, Michael and Davies, Jamie A. and Nc{-}Iuphar},
     title = {The {IUPHAR/BPS} Guide to {PHARMACOLOGY} in 2018: updates and expansion
                    to encompass the new guide to {IMMUNOPHARMACOLOGY}},
     journal = {Nucleic Acids Research},
     volume = {46},
     number = {Database-Issue},
     pages = {D1091--D1106},
     year = {2018},
     url = {https://doi.org/10.1093/nar/gkx1121},
     doi = {10.1093/nar/gkx1121}
   }
   

2017

1. Lost Silence: An emergency response early detection service through continuous processing of telecommunication data streams
   Zhou, Qianru and McLaughlin, Stephen and Gray, Alasdair J G and Wu, Shangbin and Wang, Chengxiang
   In Web Stream Processing 2017, Vienna, Austria, 2017
   

   Early detection of significant traumatic events, e.g. terrorist events, ship capsizes, is important to ensure that a prompt emergency response can occur. In the modern world telecommunication systems can and do play a key role in ensuring a successful emergency response by detecting such incidents through significant changes in calls and access to the networks. In this paper a methodology is illustrated to detect such incidents immediately (with the delay in the order of milliseconds), by processing semantically annotated streams of data in cellular telecommunication systems. In our methodology, live information of phones’ positions and status are encoded as RDF streams. We propose an algorithm that processes streams of RDF annotated telecommunication data to detect abnormality. Our approach is exemplified in the context of capsize of a passenger cruise ship but is readily translatable to other incidents. Our evaluation results show that with properly chosen window size, such incidents can be detected effectively.

   @inproceedings{ZhouEtal2017:LostSilence:WSP2017,
     author = {Zhou, Qianru and McLaughlin, Stephen and Gray, Alasdair J G and Wu, Shangbin and Wang, Chengxiang},
     title = {Lost Silence: An emergency response early detection service through continuous processing of telecommunication data streams},
     optcrossref = {},
     optkey = {},
     booktitle = {Web Stream Processing 2017},
     year = {2017},
     opteditor = {},
     optvolume = {},
     optnumber = {},
     optseries = {},
     optpages = {},
     month = oct,
     address = {Vienna, Austria},
     optorganization = {},
     optpublisher = {},
     optnote = {},
     url = {http://ceur-ws.org/Vol-1936/paper-03.pdf},
     optannote = {}
   }
   
2. Bioschemas: From Potato Salad to Protein Annotation
   Gray, Alasdair J. G. and Goble, Carole A. and Jimenez, Rafael
   In Proceedings of the ISWC 2017 Posters & Demonstrations and Industry Tracks co-located with 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 23rd - to - 25th, 2017., CEUR Workshop Proceedings, 1963, CEUR-WS.org, 2017
   (Poster paper)
   

   The life sciences have a wealth of data resources with a wide range of overlapping content. Key repositories, such as UniProt for protein data or Entrez Gene for gene data, are well known and their content easily discovered through search engines. However, there is a long-tail of bespoke datasets with important content that are not so prominent in search results. Building on the success of Schema.org for making a wide range of structured web content more discoverable and interpretable, e.g. food recipes, the Bioschemas community (http://bioschemas.org) aim to make life sciences datasets more findable by encouraging data providers to embed Schema.org markup in their resources.

   @inproceedings{Gray:BioschemasPotatoSalad:ISWC2017,
     author = {Gray, Alasdair J. G. and Goble, Carole A. and Jimenez, Rafael},
     booktitle = {Proceedings of the {ISWC} 2017 Posters {\&} Demonstrations and Industry Tracks co-located with 16th International Semantic Web Conference {(ISWC} 2017), Vienna, Austria, October 23rd - to - 25th, 2017.},
     month = oct,
     note = {(Poster paper)},
     publisher = {CEUR-WS.org},
     series = {{CEUR} Workshop Proceedings},
     title = {Bioschemas: From Potato Salad to Protein Annotation},
     url = {http://ceur-ws.org/Vol-1963/paper579.pdf},
     volume = {1963},
     year = {2017}
   }
   
3. Systematically corrupting data to assess data linkage quality
   Alsadeeqi, Ahmad and Gray, Alasdair J G
   In The Systematic Linking of Historical Records, University of Guelph, Guelph, Canada, 2017
   Workshop website \urlhttp://recordlink.org/
   

   Computer algorithms use string matching techniques to assess how likely two historical records are to be the same. The quality of linkage is unclear without knowing the correct links or ground truth. Synthetically generated datasets for which ground truth is known are helpful but the data typically are too clean to be representative of historical records. We assess data linkage algorithms under different data quality scenarios, e.g. with errors typical of historical transcriptions. A data corrupting model injects four types of mistakes: character level (e.g. an f is represented as an s – OCR Corruptions), attribute level (e.g. male changed to female due to false entry), record level (e.g. missing records), and group of records level (e.g. coffee spilt over a page, lost parish records in fire). We then evaluate record linkage algorithms over synthetically generated datasets with known ground truth and data corruptions matching a given profile.

   @inproceedings{alsadeeqiGray:systematicCorruption:2017,
     author = {Alsadeeqi, Ahmad and Gray, Alasdair J G},
     title = {Systematically corrupting data to assess data linkage quality},
     optcrossref = {},
     optkey = {},
     booktitle = {The Systematic Linking of Historical Records},
     year = {2017},
     opteditor = {},
     optvolume = {},
     optnumber = {},
     optseries = {},
     optpages = {},
     month = may,
     address = {University of Guelph, Guelph, Canada},
     optorganization = {},
     optpublisher = {},
     note = {Workshop website \url{http://recordlink.org/}},
     optannote = {}
   }
   
4. Interoperability and FAIRness through a novel combination of Web technologies
   Wilkinson, Mark D. and Verborgh, Ruben and da Silva Santos, Luiz Olavo Bonino and Clark, Tim and Swertz, Morris A. and Kelpin, Fleur D. L. and Gray, Alasdair J. G. and Schultes, Erik A. and van Mulligen, Erik M. and Ciccarese, Paolo and Kuzniar, Arnold and Gavai, Anand and Thompson, Mark and Kaliyaperumal, Rajaram and Bolleman, Jerven T. and Dumontier, Michel
   PeerJ Computer Science, 3:e110, 2017
   

   Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved at the level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.

   @article{Wilkinson:InteropFAIRWebTech:PeerJ2017,
     author = {Wilkinson, Mark D. and Verborgh, Ruben and da Silva Santos, Luiz Olavo Bonino and Clark, Tim and Swertz, Morris A. and Kelpin, Fleur D. L. and Gray, Alasdair J. G. and Schultes, Erik A. and van Mulligen, Erik M. and Ciccarese, Paolo and Kuzniar, Arnold and Gavai, Anand and Thompson, Mark and Kaliyaperumal, Rajaram and Bolleman, Jerven T. and Dumontier, Michel},
     title = {Interoperability and FAIRness through a novel combination of Web technologies},
     journal = {PeerJ Computer Science},
     volume = {3},
     pages = {e110},
     year = {2017},
     url = {https://doi.org/10.7717/peerj-cs.110},
     doi = {10.7717/peerj-cs.110}
   }
   

2016

1. Describing Datasets with the Health Care and Life Sciences Community Profile
   Gray, Alasdair J. G. and Dumontier, Michel and Marshall, M. Scott
   In Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2016), Amsterdam, The Netherlands, 2016
   (Tutorial)
   

   @inproceedings{Gray:HCLS:SWAT4LSTutorial2016,
     address = {Amsterdam, The Netherlands},
     author = {Gray, Alasdair J. G. and Dumontier, Michel and Marshall, M. Scott},
     booktitle = {Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2016)},
     month = dec,
     note = {(Tutorial)},
     title = {Describing Datasets with the Health Care and Life Sciences Community Profile},
     year = {2016}
   }
   
2. Validata: A tool for testing profile conformance
   Gray, Alasdair J. G.
   In Smart Descriptions & Smarter Vocabularies (SDSVoc), Amsterdam, The Netherlands, 2016
   

   Validata is an online web application for validating a dataset description expressed in RDF against a community profile expressed as a Shape Expression (ShEx). Additionally it provides an API for programmatic access to the validator. Validata is capable of being used for multiple community agreed standards, e.g. DCAT, the HCLS community profile, or the Open PHACTS guidelines, and there are currently deployments to support each of these. Validata can be easily repurposed for different deployments by providing it with a new ShEx schema. The Validata code is available from GitHub.

   @inproceedings{Gray2016SDSVocValidata,
     author = {Gray, Alasdair J. G.},
     title = {Validata: A tool for testing profile conformance},
     optcrossref = {},
     optkey = {},
     booktitle = {Smart Descriptions \& Smarter Vocabularies (SDSVoc)},
     year = {2016},
     opteditor = {},
     optvolume = {},
     optnumber = {},
     optseries = {},
     optpages = {},
     month = nov,
     address = {Amsterdam, The Netherlands},
     optorganization = {},
     optpublisher = {},
     optnote = {},
     url = {https://www.w3.org/2016/11/sdsvoc/SDSVoc16_paper_2},
     optannote = {}
   }
   
3. The HCLS Community Profile: Describing Datasets, Versions, and Distributions
   Dumontier, Michel and Gray, Alasdair J. G. and Marshall, M. Scott
   In Smart Descriptions & Smarter Vocabularies (SDSVoc), Amsterdam, The Netherlands, 2016
   

   Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting HCLS community profile covers elements of description, identification, attribution, versioning, provenance, and content summarization. The HCLS community profile reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets. The goal of this presentation is to give an overview of the HCLS Community Profile and explain how it extends and builds upon other approaches.

   @inproceedings{Gray2016SDSVocHCLS,
     author = {Dumontier, Michel and Gray, Alasdair J. G. and Marshall, M. Scott},
     title = {The {HCLS} Community Profile: Describing Datasets, Versions, and Distributions},
     optcrossref = {},
     optkey = {},
     booktitle = {Smart Descriptions \& Smarter Vocabularies (SDSVoc)},
     year = {2016},
     opteditor = {},
     optvolume = {},
     optnumber = {},
     optseries = {},
     optpages = {},
     month = nov,
     address = {Amsterdam, The Netherlands},
     optorganization = {},
     optpublisher = {},
     optnote = {},
     url = {https://www.w3.org/2016/11/sdsvoc/SDSVoc16_paper_3},
     optannote = {}
   }
   
4. The Semantic Web - ISWC 2016 - 15th International Semantic Web Conference, Kobe, Japan, October 17-21, 2016, Proceedings, Part II
   Groth, Paul T. and Simperl, Elena and Gray, Alasdair J. G. and Sabou, Marta and Krötzsch, Markus and Lécué, Freddy and Flöck, Fabian and Gil, Yolanda
   Lecture Notes in Computer Science, 9982, 2016
   ISBN: 978-3-319-46546-3
   

   @proceedings{iswc2016-2,
     editor = {Groth, Paul T. and Simperl, Elena and Gray, Alasdair J. G. and Sabou, Marta and Kr{\"{o}}tzsch, Markus and L{\'{e}}cu{\'{e}}, Freddy and Fl{\"{o}}ck, Fabian and Gil, Yolanda},
     title = {The Semantic Web - {ISWC} 2016 - 15th International Semantic Web Conference,
                    Kobe, Japan, October 17-21, 2016, Proceedings, Part {II}},
     series = {Lecture Notes in Computer Science},
     volume = {9982},
     month = oct,
     year = {2016},
     url = {http://dx.doi.org/10.1007/978-3-319-46547-0},
     doi = {10.1007/978-3-319-46547-0},
     isbn = {978-3-319-46546-3}
   }
   
5. The Semantic Web - ISWC 2016 - 15th International Semantic Web Conference, Kobe, Japan, October 17-21, 2016, Proceedings, Part I
   Groth, Paul T. and Simperl, Elena and Gray, Alasdair J. G. and Sabou, Marta and Krötzsch, Markus and Lécué, Freddy and Flöck, Fabian and Gil, Yolanda
   Lecture Notes in Computer Science, 9981, 2016
   ISBN: 978-3-319-46522-7
   

   @proceedings{iswc2016-1,
     editor = {Groth, Paul T. and Simperl, Elena and Gray, Alasdair J. G. and Sabou, Marta and Kr{\"{o}}tzsch, Markus and L{\'{e}}cu{\'{e}}, Freddy and Fl{\"{o}}ck, Fabian and Gil, Yolanda},
     title = {The Semantic Web - {ISWC} 2016 - 15th International Semantic Web Conference,
                    Kobe, Japan, October 17-21, 2016, Proceedings, Part {I}},
     series = {Lecture Notes in Computer Science},
     volume = {9981},
     month = oct,
     year = {2016},
     url = {http://dx.doi.org/10.1007/978-3-319-46523-4},
     doi = {10.1007/978-3-319-46523-4},
     isbn = {978-3-319-46522-7}
   }
   
6. The health care and life sciences community profile for dataset descriptions
   Dumontier, Michel and Gray, Alasdair JG and Marshall, M Scott and Alexiev, Vladimir and Ansell, Peter and Bader, Gary and Baran, Joachim and Bolleman, Jerven T and Callahan, Alison and Cruz-Toledo, José and others
   PeerJ, 4:e2331, PeerJ Inc., 2016
   

   Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.

   @article{Dumontier:HCLS-datadesc:PeerJ2016,
     title = {The health care and life sciences community profile for dataset descriptions},
     author = {Dumontier, Michel and Gray, Alasdair JG and Marshall, M Scott and Alexiev, Vladimir and Ansell, Peter and Bader, Gary and Baran, Joachim and Bolleman, Jerven T and Callahan, Alison and Cruz-Toledo, Jos{\'e} and others},
     journal = {PeerJ},
     volume = {4},
     pages = {e2331},
     year = {2016},
     month = aug,
     url = {https://doi.org/10.7717/peerj.2331},
     doi = {10.7717/peerj.2331},
     publisher = {PeerJ Inc.}
   }
   
7. Administrative social science data: The challenge of reproducible research
   Playford, Christopher J and Gayle, Vernon and Connelly, Roxanne and Gray, Alasdair JG
   Big Data and Society, 3(2):2053951716684143, 2016
   

   Powerful new social science data resources are emerging. One particularly important source is administrative data, which were originally collected for organisational purposes but often contain information that is suitable for social science research. In this paper we outline the concept of reproducible research in relation to micro-level administrative social science data. Our central claim is that a planned and organised workflow is essential for high quality research using micro-level administrative social science data. We argue that it is essential for researchers to share research code, because code sharing enables the elements of reproducible research. First, it enables results to be duplicated and therefore allows the accuracy and validity of analyses to be evaluated. Second, it facilitates further tests of the robustness of the original piece of research. Drawing on insights from computer science and other disciplines that have been engaged in e-Research we discuss and advocate the use of Git repositories to provide a useable and effective solution to research code sharing and rendering social science research using micro-level administrative data reproducible.

   @article{Playford:AdminSocSciRep:BDS2016,
     author = {Playford, Christopher J and Gayle, Vernon and Connelly, Roxanne and Gray, Alasdair JG},
     title = {Administrative social science data: The challenge of reproducible research},
     journal = {Big Data and Society},
     volume = {3},
     number = {2},
     pages = {2053951716684143},
     year = {2016},
     doi = {10.1177/2053951716684143},
     url = {https://doi.org/10.1177/2053951716684143},
     eprint = {https://doi.org/10.1177/2053951716684143}
   }
   
8. The FAIR Guiding Principles for scientific data management and stewardship
   Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others
   Scientific data, 3(1):1–9, Nature Publishing Group, 2016
   

   There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

   @article{Wilkinson:FAIRPrinciples:SciData2016,
     title = {The FAIR Guiding Principles for scientific data management and stewardship},
     author = {Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others},
     journal = {Scientific data},
     volume = {3},
     number = {1},
     pages = {1--9},
     year = {2016},
     publisher = {Nature Publishing Group},
     doi = {10.1038/sdata.2016.18}
   }
   

2015

1. Dataset Descriptions: HCLS Community Profile
   Gray, A. J. G. and Baran, Joachim and Marshall, M Scott and Dumontier (Eds), Michel
   W3C Interest Group Note. World Wide Web Consortium. may, 2015
   

   @techreport{Gray2015HCLS,
     author = {Gray, A. J. G. and Baran, Joachim and Marshall, M Scott and {Dumontier (Eds)}, Michel},
     month = may,
     publisher = {World Wide Web Consortium},
     type = {{W3C Interest Group Note}},
     title = {{Dataset Descriptions: {HCLS} Community Profile}},
     year = {2015},
     url = {https://www.w3.org/TR/hcls-dataset/}
   }
   

2014

1. Bring Your Own Data Workshops: A Mechanism to Aid Data Owners to Comply with Linked Data Best Practices
   Roos, Marco and Gray, Alasdair J. G. and Waagmeester, Andra and Thompson, Mark and Kaliyaperumal, Rajaram and van der Horst, Eelke and Mons, Barend and Wilkinson, Mark
   In Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, Berlin, Germany, December 9-11, 2014., CEUR Workshop Proceedings, 1320, CEUR-WS.org, 2014
   

   @inproceedings{DBLP:conf/swat4ls/RoosGWTKHMW14,
     author = {Roos, Marco and Gray, Alasdair J. G. and Waagmeester, Andra and Thompson, Mark and Kaliyaperumal, Rajaram and van der Horst, Eelke and Mons, Barend and Wilkinson, Mark},
     title = {Bring Your Own Data Workshops: {A} Mechanism to Aid Data Owners to
                    Comply with Linked Data Best Practices},
     booktitle = {Proceedings of the 7th International Workshop on Semantic Web Applications
                    and Tools for Life Sciences, Berlin, Germany, December 9-11, 2014.},
     series = {{CEUR} Workshop Proceedings},
     volume = {1320},
     publisher = {CEUR-WS.org},
     month = dec,
     year = {2014},
     url = {http://ceur-ws.org/Vol-1320/paper\_36.pdf}
   }
   
2. A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings
   Hussain, Sajjad and Sun, Hong and Erturkmen, Gokce Banu Laleci and Yuksel, Mustafa and Mead, Charles and Gray, Alasdair J G and Forsberg, Kerstin
   In Context Interpretation and Meaning, Riva del Garda, Italy, 2014
   

   Use of medical terminologies and mappings across them are consid- ered to be crucial pre-requisites for achieving interoperable eHealth applica- tions. However, experiences from several research projects have demonstrated that the mappings are not enough. Also the context of the mappings is needed to enable interpretation of the meaning of the mappings. Built upon these experi- ences, we introduce a semantic framework for representing, evaluating and uti- lizing terminology mappings together with the context in terms of the justifica- tions for, and the provenance of, the mappings. The framework offers a plat- form for i) performing various mappings strategies, ii) representing terminology mappings together with their provenance information, and iii) enabling termi- nology reasoning for inferring both new and erroneous mappings. We present the results of the introduced framework using the SALUS project where we evaluated the quality of both existing and inferred terminology mappings among standard terminologies.

   @inproceedings{Hussain2014CIM,
     address = {Riva del Garda, Italy},
     author = {Hussain, Sajjad and Sun, Hong and Erturkmen, Gokce Banu Laleci and Yuksel, Mustafa and Mead, Charles and Gray, Alasdair J G and Forsberg, Kerstin},
     booktitle = {Context Interpretation and Meaning},
     title = {{A Justification-based Semantic Framework for Representing , Evaluating and Utilizing Terminology Mappings}},
     url = {http://www.macs.hw.ac.uk/~fm206/cim14/cim20140_submission_2.pdf},
     month = oct,
     year = {2014}
   }
   
3. Capturing Provenance for a Linkset of Convenience
   Jupp, Simon and Malone, James and Gray, Alasdair J. G.
   In Proceedings of the 4th Workshop on Linked Science 2014 - Making Sense Out of Data (LISC2014) co-located with the 13th International Semantic Web Conference (ISWC 2014), Riva del Garda, Italy, October 19, 2014., pages 71–75, 2014
   

   Biological interactions such as those between genes and proteins are complex and require intricate OWL models. However, direct links between biological entities can support search and data integration. In this paper we introduce linksets of convenience that capture these direct links. We show the provenance statements required to track the derivation of such linksets; linking them back to the full biological justification.

   @inproceedings{JuppMG14,
     author = {Jupp, Simon and Malone, James and Gray, Alasdair J. G.},
     title = {Capturing Provenance for a Linkset of Convenience},
     booktitle = {Proceedings of the 4th Workshop on Linked Science 2014 - Making Sense
                    Out of Data {(LISC2014)} co-located with the 13th International Semantic
                    Web Conference {(ISWC} 2014), Riva del Garda, Italy, October 19, 2014.},
     pages = {71--75},
     month = oct,
     year = {2014},
     url = {http://ceur-ws.org/Vol-1282/lisc2014_submission_7.pdf}
   }
   
4. Scientific Lenses to Support Multiple Views over Linked Chemistry Data
   Batchelor, Colin R. and Brenninkmeijer, Christian Y. A. and Chichester, Christine and Davies, Mark and Digles, Daniela and Dunlop, Ian and Evelo, Chris T. A. and Gaulton, Anna and Goble, Carole A. and Gray, Alasdair J. G. and Groth, Paul T. and Harland, Lee and Karapetyan, Karen and Loizou, Antonis and Overington, John P. and Pettifer, Steve and Steele, Jon and Stevens, Robert and Tkachenko, Valery and Waagmeester, Andra and Williams, Antony J. and Willighagen, Egon L.
   In The Semantic Web - ISWC 2014 - 13th International Semantic Web Conference, Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part I, Lecture Notes in Computer Science, 8796, pages 98–113, Springer, 2014
   (Alphabetical authorship)
   

   @inproceedings{Batchelor:SciLenses:ISWC2014,
     author = {Batchelor, Colin R. and Brenninkmeijer, Christian Y. A. and Chichester, Christine and Davies, Mark and Digles, Daniela and Dunlop, Ian and Evelo, Chris T. A. and Gaulton, Anna and Goble, Carole A. and Gray, Alasdair J. G. and Groth, Paul T. and Harland, Lee and Karapetyan, Karen and Loizou, Antonis and Overington, John P. and Pettifer, Steve and Steele, Jon and Stevens, Robert and Tkachenko, Valery and Waagmeester, Andra and Williams, Antony J. and Willighagen, Egon L.},
     title = {Scientific Lenses to Support Multiple Views over Linked Chemistry
                    Data},
     booktitle = {The Semantic Web - {ISWC} 2014 - 13th International Semantic Web Conference,
                    Riva del Garda, Italy, October 19-23, 2014. Proceedings, Part {I}},
     series = {Lecture Notes in Computer Science},
     volume = {8796},
     pages = {98--113},
     publisher = {Springer},
     month = oct,
     year = {2014},
     note = {(Alphabetical authorship)},
     url = {https://doi.org/10.1007/978-3-319-11964-9\_7},
     doi = {10.1007/978-3-319-11964-9\_7}
   }
   
5. Help me describe my data: A demonstration of the Open PHACTS VoID Editor
   Goble, Carole A. and Gray, Alasdair J. G. and Tatakis, Eleftherios
   In Proceedings of the ISWC 2014 Posters & Demonstrations Track a track within the 13th International Semantic Web Conference, ISWC 2014, Riva del Garda, Italy, October 21, 2014., CEUR Workshop Proceedings, 1272, pages 29–32, CEUR-WS.org, 2014
   (Demo paper)
   

   @inproceedings{Goble:VoIDEditor:ISWC2014,
     author = {Goble, Carole A. and Gray, Alasdair J. G. and Tatakis, Eleftherios},
     booktitle = {Proceedings of the {ISWC} 2014 Posters {\&} Demonstrations Track a track within the 13th International Semantic Web Conference, {ISWC} 2014, Riva del Garda, Italy, October 21, 2014.},
     editor = {Horridge, Matthew and Rospocher, Marco and van Ossenbruggen, Jacco},
     month = oct,
     note = {(Demo paper)},
     pages = {29--32},
     publisher = {CEUR-WS.org},
     series = {{CEUR} Workshop Proceedings},
     title = {Help me describe my data: {A} demonstration of the Open {PHACTS} VoID Editor},
     url = {http://ceur-ws.org/Vol-1272/paper\_33.pdf},
     volume = {1272},
     year = {2014}
   }
   
6. A Framework for Evaluating and Utilizing Medical Terminology Mappings
   Hussain, Sajjad and Sun, Hong and Sinaci, Ali Anil and Erturkmen, Gokce Banu Laleci and Mead, Charles N. and Gray, Alasdair J. G. and McGuinness, Deborah L. and Prud’hommeaux, Eric and Daniel, Christel and Forsberg, Kerstin
   In e-Health - For Continuity of Care - Proceedings of MIE2014, the 25th European Medical Informatics Conference, Istanbul, Turkey, August 31 - September 3, 2014, Studies in Health Technology and Informatics, 205, pages 594–598, IOS Press, 2014
   

   @inproceedings{Hussain:MedicalMappings:MIE2014,
     author = {Hussain, Sajjad and Sun, Hong and Sinaci, Ali Anil and Erturkmen, Gokce Banu Laleci and Mead, Charles N. and Gray, Alasdair J. G. and McGuinness, Deborah L. and Prud'hommeaux, Eric and Daniel, Christel and Forsberg, Kerstin},
     title = {A Framework for Evaluating and Utilizing Medical Terminology Mappings},
     booktitle = {e-Health - For Continuity of Care - Proceedings of MIE2014, the 25th
                    European Medical Informatics Conference, Istanbul, Turkey, August
                    31 - September 3, 2014},
     series = {Studies in Health Technology and Informatics},
     volume = {205},
     pages = {594--598},
     publisher = {{IOS} Press},
     month = sep,
     year = {2014},
     url = {https://doi.org/10.3233/978-1-61499-432-9-594},
     doi = {10.3233/978-1-61499-432-9-594}
   }
   
7. SensorBench: benchmarking approaches to processing wireless sensor network data
   Galpin, Ixent and Stokes, Alan B. and Valkanas, George and Gray, Alasdair J. G. and Paton, Norman W. and Fernandes, Alvaro A. A. and Sattler, Kai-Uwe and Gunopulos, Dimitrios
   In Conference on Scientific and Statistical Database Management, SSDBM ’14, Aalborg, Denmark, June 30 - July 02, 2014, pages 21:1–21:12, ACM, 2014
   

   @inproceedings{Galpin:SensorBench:SSDBM2014,
     author = {Galpin, Ixent and Stokes, Alan B. and Valkanas, George and Gray, Alasdair J. G. and Paton, Norman W. and Fernandes, Alvaro A. A. and Sattler, Kai{-}Uwe and Gunopulos, Dimitrios},
     title = {SensorBench: benchmarking approaches to processing wireless sensor
                    network data},
     booktitle = {Conference on Scientific and Statistical Database Management, {SSDBM}
                    '14, Aalborg, Denmark, June 30 - July 02, 2014},
     pages = {21:1--21:12},
     publisher = {{ACM}},
     month = jun,
     year = {2014},
     url = {https://doi.org/10.1145/2618243.2618252},
     doi = {10.1145/2618243.2618252}
   }
   
8. Scientific Lenses over Linked Chemistry Data using BridgeDb and the Open PHACTS Chemistry Registration System
   Batchelor, Colin and Brenninkmeijer, Christian and Evelo, Chris and Goble, Carole and Gray, Alasdair and Karapetyan, Ken and Tkachenko, Valery and Willighagen, Egon
   In 10th ICCS, International Conference on Chemical Structures, Noordwijkerhout, the Netherlands, 2014
   (Extended abstract)
   

   @inproceedings{Batchelor:chem-lenses:ChemStruct2014,
     address = {Noordwijkerhout, the Netherlands},
     author = {Batchelor, Colin and Brenninkmeijer, Christian and Evelo, Chris and Goble, Carole and Gray, Alasdair and Karapetyan, Ken and Tkachenko, Valery and Willighagen, Egon},
     booktitle = {10th ICCS, International Conference on Chemical Structures},
     month = jun,
     note = {(Extended abstract)},
     title = {Scientific Lenses over Linked Chemistry Data using BridgeDb and the Open PHACTS Chemistry Registration System},
     year = {2014}
   }
   
9. Dataset Descriptions for Linked Data Systems
   Gray, Alasdair J. G.
   IEEE Internet Computing, 18(4):66–69, 2014
   

   @article{DBLP:journals/internet/Gray14,
     author = {Gray, Alasdair J. G.},
     title = {Dataset Descriptions for Linked Data Systems},
     journal = {{IEEE} Internet Computing},
     volume = {18},
     number = {4},
     pages = {66--69},
     year = {2014},
     url = {https://doi.org/10.1109/MIC.2014.66},
     doi = {10.1109/MIC.2014.66}
   }
   
10. Applying linked data approaches to pharmacology: Architectural decisions and implementation
    Gray, Alasdair J. G. and Groth, Paul T. and Loizou, Antonis and Askjaer, Sune and Brenninkmeijer, Christian Y. A. and Burger, Kees and Chichester, Christine and Evelo, Chris T. A. and Goble, Carole A. and Harland, Lee and Pettifer, Steve and Thompson, Mark and Waagmeester, Andra and Williams, Antony J.
    Semantic Web Journal, 5(2):101–113, 2014
    

    The discovery of new medicines requires pharmacologists to interact with a number of information sources ranging from tabular data to scientific papers, and other specialized formats. In this application report, we describe a linked data platform for integrating multiple pharmacology datasets that form the basis for several drug discovery applications. The functionality offered by the platform has been drawn from a collection of prioritised drug discovery business questions created as part of the Open PHACTS project, a collaboration of research institutions and major pharmaceutical companies. We describe the architecture of the platform focusing on seven design decisions that drove its development with the aim of informing others developing similar software in this or other domains. The utility of the platform is demonstrated by the variety of drug discovery applications being built to access the integrated data.

    @article{Gray:OPS:SWJ,
      author = {Gray, Alasdair J. G. and Groth, Paul T. and Loizou, Antonis and Askjaer, Sune and Brenninkmeijer, Christian Y. A. and Burger, Kees and Chichester, Christine and Evelo, Chris T. A. and Goble, Carole A. and Harland, Lee and Pettifer, Steve and Thompson, Mark and Waagmeester, Andra and Williams, Antony J.},
      title = {Applying linked data approaches to pharmacology: Architectural decisions
                     and implementation},
      journal = {Semantic Web Journal},
      volume = {5},
      number = {2},
      pages = {101--113},
      year = {2014},
      url = {https://doi.org/10.3233/SW-2012-0088},
      doi = {10.3233/SW-2012-0088}
    }
    
11. API-centric Linked Data integration: The Open PHACTS Discovery Platform case study
    Groth, Paul T. and Loizou, Antonis and Gray, Alasdair J. G. and Goble, Carole A. and Harland, Lee and Pettifer, Steve
    Journal of Web Semantics, 29:12–18, 2014
    

    @article{DBLP:journals/ws/GrothLGGHP14,
      author = {Groth, Paul T. and Loizou, Antonis and Gray, Alasdair J. G. and Goble, Carole A. and Harland, Lee and Pettifer, Steve},
      title = {API-centric Linked Data integration: The Open {PHACTS} Discovery Platform
                     case study},
      journal = {Journal of Web Semantics},
      volume = {29},
      pages = {12--18},
      year = {2014},
      url = {https://doi.org/10.1016/j.websem.2014.03.003},
      doi = {10.1016/j.websem.2014.03.003}
    }
    

2013

1. Open PHACTS Explorer 2: Bringing the web to the semantic web
   Dunlop, Ian and Ramgolam, Rishi and Pettifer, Steve and Gray, Alasdair J. G. and Eales, James and Goble, Carole and Velterop, Jan
   In Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013), Edinburgh, UK, CEUR-WS, 2013
   

   @inproceedings{Dunlop2013,
     author = {Dunlop, Ian and Ramgolam, Rishi and Pettifer, Steve and Gray, Alasdair J. G. and Eales, James and Goble, Carole and Velterop, Jan},
     title = {Open PHACTS Explorer 2: Bringing the web to the semantic web},
     optcrossref = {},
     optkey = {},
     booktitle = {Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013)},
     year = {2013},
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     month = dec,
     address = {Edinburgh, UK},
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     optnote = {},
     optannote = {},
     url = {http://ceur-ws.org/Vol-1114/Demo_Dunlop.pdf}
   }
   
2. Computing Identity Co-Reference Across Drug Discovery Datasets
   Brenninkmeijer, Christian Y. A. and Dunlop, Ian and Goble, Carole and Gray, Alasdair J. G. and Pettifer, Steve and Stevens, Robert
   In Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013), Edinburgh, UK, CEUR-WS, 2013
   

   @inproceedings{Brenn2013SWAT4LS,
     author = {Brenninkmeijer, Christian Y. A. and Dunlop, Ian and Goble, Carole and Gray, Alasdair J. G. and Pettifer, Steve and Stevens, Robert},
     title = {Computing Identity Co-Reference Across Drug Discovery Datasets},
     optcrossref = {},
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     booktitle = {Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013)},
     year = {2013},
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     month = dec,
     address = {Edinburgh, UK},
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     optannote = {},
     url = {http://ceur-ws.org/Vol-1114/Session4_Brenninkmeijer.pdf}
   }
   
3. The Hitch-hikers Guide to the Semantic Web
   Gray, Alasdair J. G. and Splendiani, Andrea
   In Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013), Edinburgh, UK, 2013
   (Tutorial)
   

   @inproceedings{Gray2013SWAT4LSTutorial,
     address = {Edinburgh, UK},
     author = {Gray, Alasdair J. G. and Splendiani, Andrea},
     booktitle = {Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2013)},
     month = dec,
     note = {(Tutorial)},
     title = {The Hitch-hikers Guide to the Semantic Web},
     year = {2013}
   }
   
4. Including Co-referent URIs in a SPARQL Query
   Brenninkmeijer, Christian Y. A. and Goble, Carole A. and Gray, Alasdair J. G. and Groth, Paul T. and Loizou, Antonis and Pettifer, Steve
   In Proceedings of the Fourth International Workshop on Consuming Linked Data, COLD 2013, Sydney, Australia, October 22, 2013, Sydney, Australia, CEUR Workshop Proceedings, 2013
   http://ceur-ws.org/Vol-1034/BrenninkmeijerEtAl_COLD2013.pdf
   

   Linked data relies on instance level links between potentially differing representations of concepts in multiple datasets. However, in large complex domains, such as pharmacology, the inter-relationship of data instances needs to consider the context (e.g. task, role) of the user and the assumptions they want to apply to the data. Such context is not taken into account in most linked data integration procedures. In this paper we argue that dataset links should be stored in a stand-off fashion, thus enabling different assumptions to be applied to the data links during query execution. We present the infrastructure developed for the Open PHACTS Discovery Platform to enable this and show through evaluation that the incurred performance cost is below the threshold of user perception.

   @inproceedings{Brenn2013COLD,
     address = {Sydney, Australia},
     author = {Brenninkmeijer, Christian Y. A. and Goble, Carole A. and Gray, Alasdair J. G. and Groth, Paul T. and Loizou, Antonis and Pettifer, Steve},
     title = {Including Co-referent URIs in a {SPARQL} Query},
     booktitle = {Proceedings of the Fourth International Workshop on Consuming Linked
                    Data, {COLD} 2013, Sydney, Australia, October 22, 2013},
     month = oct,
     year = {2013},
     publisher = {CEUR Workshop Proceedings},
     note = {http://ceur-ws.org/Vol-1034/BrenninkmeijerEtAl_COLD2013.pdf},
     url = {http://ceur-ws.org/Vol-1034/BrenninkmeijerEtAl_COLD2013.pdf}
   }
   
5. Incorporating Commercial and Private Data into an Open Linked Data Platform for Drug Discovery
   Goble, Carole A. and Gray, Alasdair J. G. and Harland, Lee and Karapetyan, Karen and Loizou, Antonis and Mikhailov, Ivan and Rankka, Yrjänä and Senger, Stefan and Tkachenko, Valery and Williams, Antony J. and Willighagen, Egon L.
   In The Semantic Web - ISWC 2013 - 12th International Semantic Web Conference, Sydney, NSW, Australia, October 21-25, 2013, Proceedings, Part II, Lecture Notes in Computer Science, 8219, pages 65–80, Springer, 2013
   

   @inproceedings{DBLP:conf/semweb/GobleGHKLMRSTWW13,
     author = {Goble, Carole A. and Gray, Alasdair J. G. and Harland, Lee and Karapetyan, Karen and Loizou, Antonis and Mikhailov, Ivan and Rankka, Yrj{\"{a}}n{\"{a}} and Senger, Stefan and Tkachenko, Valery and Williams, Antony J. and Willighagen, Egon L.},
     title = {Incorporating Commercial and Private Data into an Open Linked Data
                    Platform for Drug Discovery},
     booktitle = {The Semantic Web - {ISWC} 2013 - 12th International Semantic Web Conference,
                    Sydney, NSW, Australia, October 21-25, 2013, Proceedings, Part {II}},
     series = {Lecture Notes in Computer Science},
     volume = {8219},
     pages = {65--80},
     publisher = {Springer},
     month = oct,
     year = {2013},
     url = {https://doi.org/10.1007/978-3-642-41338-4\_5},
     doi = {10.1007/978-3-642-41338-4\_5}
   }
   
6. Declarative In-Network Sensor Data Analysis
   Valkanas, George and Galpin, Ixent and Gray, Alasdair J. G. and Fernandes, Alvaro A. A. and Paton, Norman W. and Gunopulos, Dimitrios
   In European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases 2013 Workshop on Languages for Data Mining and Machine Learning, Prague, Czech Republic, 2013
   

   @inproceedings{Valkanas:in-network-analysis:LML2013,
     author = {Valkanas, George and Galpin, Ixent and Gray, Alasdair J. G. and Fernandes, Alvaro A. A. and Paton, Norman W. and Gunopulos, Dimitrios},
     title = {Declarative In-Network Sensor Data Analysis},
     optcrossref = {},
     optkey = {},
     booktitle = {European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases 2013 Workshop on Languages for Data Mining and Machine Learning},
     year = {2013},
     opteditor = {},
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     optpages = {},
     month = sep,
     address = {Prague, Czech Republic},
     optorganization = {},
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     optnote = {},
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     url = {http://dtai.cs.kuleuven.be/lml/papers/lml2013_declarative_sensor.pdf}
   }
   
7. Scientific Lenses: An Approach to Dynamically Vary the Relationships between Datasets
   Brenninkmeijer, C. and Evelo, C. and Goble, C. and Gray, A.J.G. and Groth, P. and Pettifer, S. and Stevens, R. and Williams, A. and Willighagen, E.
   In Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2013), Berlin, Germany, 2013
   (Poster paper)
   

   @inproceedings{brenninkmeijer:lenses:ismbeccb2013,
     address = {Berlin, Germany},
     author = {Brenninkmeijer, C. and Evelo, C. and Goble, C. and Gray, A.J.G. and Groth, P. and Pettifer, S. and Stevens, R. and Williams, A. and Willighagen, E.},
     booktitle = {Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2013)},
     month = jul,
     note = {(Poster paper)},
     title = {Scientific Lenses: An Approach to Dynamically Vary the Relationships between Datasets},
     year = {2013}
   }
   
8. Open PHACTS: meaningful linking of preclinical drug discovery knowledge
   Willighagen, Egon and Brenninkmeijer, Christian Y. A. and Evelo, Chris T. and Gray, Alasdair J. G. and Goble, Carole and Harland, Lee and Waagmeester, Andra and Williams, Antony J.
   In 245th American Chemcial Society National Meeting and Exposition, New Orleans, LA, USA, 2013
   (Extended abstract)
   

   @inproceedings{Willighagen:2013we,
     address = {New Orleans, LA, USA},
     author = {Willighagen, Egon and Brenninkmeijer, Christian Y. A. and Evelo, Chris T. and Gray, Alasdair J. G. and Goble, Carole and Harland, Lee and Waagmeester, Andra and Williams, Antony J.},
     booktitle = {245th American Chemcial Society National Meeting and Exposition},
     month = apr,
     note = {(Extended abstract)},
     title = {{Open PHACTS}: meaningful linking of preclinical drug discovery knowledge},
     year = {2013}
   }
   
9. Enabling Drug Discovery Applications Through a Linked Data Platform
   Gray, A.J.G.
   In Conference on Semantics in Healthcare and Life Sciences, Boston, MA, USA, 2013
   (Technology talk)
   

   We present the Open PHACTS linked data platform that is being developed to support a wide range of novel drug discovery applications. The functionality offered by the platform has been drawn from a collection of prioritised drug discovery business questions created as part of the Open PHACTS project, a collaboration of research institutions and major pharmaceutical companies. The discovery of new medicines requires pharmacologists to interact with a number of data sources; ranging from data on chemical compounds to their interactions with targets. The linked data platform provides an integrated view over data retrieved from several complementary, but overlapping, data sources Key features of the Open PHACTS linked data platform are: 1) Domain specific API making drug discovery linked data available for a diverse range of applications without requiring the application developers to become knowledgeable of semantic web standards such as SPARQL; 2) Just-in-time identity resolution and alignment across datasets enabling a variety of entry points to the data and ultimately to support different integrated views of the data; 3) Centrally cached copies of public datasets to support interactive response times for user-facing applications. The Open PHACTS platform is hosted by OpenLink using the Virtuoso triplestore. This is enabling us to provide the security and privacy guarantees required by pharmaceutical companies. We have recently begun beta testing of the platform with our associated partners and anticipate a full public roll-out later in 2013. The utility of the linked data platform is demonstrated by the variety of drug discovery applications being built to access the integrated data.

   @inproceedings{gray:OPS:cshals2013,
     address = {Boston, MA, USA},
     author = {Gray, A.J.G.},
     booktitle = {Conference on Semantics in Healthcare and Life Sciences},
     month = feb,
     note = {(Technology talk)},
     title = {Enabling Drug Discovery Applications Through a Linked Data Platform},
     year = {2013}
   }
   
10. Guidelines for Nanopublications
    Gray, A.J.G. and Chichester, C. and Burger, K. and Kotoulas, S. and Loizou, A. and Tkachenko, V. and Waagmeester, A. and Askjaer, S. and Pettifer, S. and Harland, L. and Haupt, C. and Batchelor, C. and Vazquez, M. and Fernández, J. María and Saito, J. and Gibson, A. and Wich, L.
    Working Draft, 1.8-20130102. Concept Web Alliance. jan, 2013
    
    

    @techreport{nanopubs,
      author = {Gray, A.J.G. and Chichester, C. and Burger, K. and Kotoulas, S. and Loizou, A. and Tkachenko, V. and Waagmeester, A. and Askjaer, S. and Pettifer, S. and Harland, L. and Haupt, C. and Batchelor, C. and Vazquez, M. and Fern\'andez, J. Mar\'ia and Saito, J. and Gibson, A. and Wich, L.},
      title = {Guidelines for Nanopublications},
      institution = {Concept Web Alliance},
      year = {2013},
      optkey = {},
      type = {Working Draft},
      number = {1.8-20130102},
      optaddress = {},
      month = jan,
      note = {},
      url = {http://nanopub.org/guidelines/working_draft/},
      optannote = {}
    }
    
11. PAV ontology: provenance, authoring and versioning
    Ciccarese, Paolo and Soiland-Reyes, Stian and Belhajjame, Khalid and Gray, Alasdair J. G. and Goble, Carole A. and Clark, Tim
    Journal of Biomedical Semantics, 4:37, 2013
    

    Background Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidence. Existing vocabularies such as Dublin Core Terms (DC Terms) and the W3C Provenance Ontology (PROV-O) are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. In particular, to track authoring and versioning information of web resources, PROV-O provides a basic methodology but not any specific classes and properties for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. Results We present the Provenance, Authoring and Versioning ontology (PAV, namespace http://purl.org/pav/): a lightweight ontology for capturing “just enough” descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the W3C PROV-O ontology to support broader interoperability. Method The initial design of the PAV ontology was driven by requirements from the AlzSWAN project with further requirements incorporated later from other projects detailed in this paper. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. Discussion We analyze and compare PAV with related approaches, namely Provenance Vocabulary (PRV), DC Terms and BIBFRAME. We identify similarities and analyze differences between those vocabularies and PAV, outlining strengths and weaknesses of our proposed model. We specify SKOS mappings that align PAV with DC Terms. We conclude the paper with general remarks on the applicability of PAV.

    @article{Ciccarese:PAV:JoBS2013,
      author = {Ciccarese, Paolo and Soiland{-}Reyes, Stian and Belhajjame, Khalid and Gray, Alasdair J. G. and Goble, Carole A. and Clark, Tim},
      title = {{PAV} ontology: provenance, authoring and versioning},
      journal = {Journal of Biomedical Semantics},
      volume = {4},
      pages = {37},
      year = {2013},
      url = {https://doi.org/10.1186/2041-1480-4-37},
      doi = {10.1186/2041-1480-4-37}
    }
    
12. Processing online crop disease warning information via sensor networks using ISA ontologies
    Jackman, Patrick and Gray, Alasdair J G and Brass, Andrew and Stevens, Robert and Shi, Ming and Scuffell, Derek and Hammersley, Simon and Grieve, Bruce
    Agricultural Engineering International: CIGR Journal, 15(3):243–251, International Commission of Agricultural and Biosystems Engineering, 2013
    

    Growing demand for food is driving the need for higher crop yields globally. Correctly anticipating the onset of damaging crop diseases is essential to achieve this goal. Considerable efforts have been made recently to develop early warning systems. However, these methods lack a direct and online measurement of the spores that attack crops. A novel disease information network has been implemented and deployed. Spore sensors have been developed and deployed. The measurements from these sensors are combined with similar measurements of important local weather readings to generate estimates of crop disease risk. It is combined with other crop disease information allowing overall local disease risk assessments and forecasts to be made. The resulting data is published through a SPARQL endpoint to support reuse and connection into the linked data cloud.

    @article{Jackman:2013Processing-Online-Crop-Disease,
      title = {Processing online crop disease warning information via sensor networks using ISA ontologies},
      keywords = {Crop disease assessment, Data queries, Investigation study assay, Online sensors, Sensor network, Web semantics},
      author = {Jackman, Patrick and Gray, Alasdair J G and Brass, Andrew and Stevens, Robert and Shi, Ming and Scuffell, Derek and Hammersley, Simon and Grieve, Bruce},
      year = {2013},
      language = {English},
      volume = {15},
      pages = {243--251},
      journal = {Agricultural Engineering International: CIGR Journal},
      issn = {1682-1130},
      publisher = {International Commission of Agricultural and Biosystems Engineering},
      number = {3}
    }
    

2012

1. Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision
   Brenninkmeijer, C. and Evelo, C. and Goble, C. and Gray, A.J.G. and Groth, P. and Pettifer, S. and Stevens, R. and Williams, A.J. and Willighagen, E.L.
   In 2nd International Workshop on Linked Science 2012 – Tackling Big Data (LISC 2012), Boston, MA, USA, 951, CEUR Workshop Proceedings, 2012
   (Alphabetic authorship)
   

   @inproceedings{Brenn2012LISC,
     address = {Boston, MA, USA},
     author = {Brenninkmeijer, C. and Evelo, C. and Goble, C. and Gray, A.J.G. and Groth, P. and Pettifer, S. and Stevens, R. and Williams, A.J. and Willighagen, E.L.},
     booktitle = {2nd International Workshop on Linked Science 2012 -- Tackling Big Data (LISC 2012)},
     note = {(Alphabetic authorship)},
     optpages = {},
     title = {Scientific Lenses over Linked Data: An approach to support task specific views of the data. A vision},
     year = {2012},
     month = nov,
     volume = {951},
     publisher = {CEUR Workshop Proceedings},
     weburl = {http://ceur-ws.org/Vol-951/paper5.pdf}
   }
   
2. Dataset descriptions for the Open Pharmacological Space
   Gray (Ed), A.J.G.
   Working Draft. Open PHACTS. oct, 2012
   
   

   @techreport{OPS-datadesc,
     author = {{Gray (Ed)}, A.J.G.},
     title = {Dataset descriptions for the Open Pharmacological Space},
     institution = {Open PHACTS},
     year = {2012},
     optkey = {},
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     optnumber = {},
     optaddress = {},
     month = oct,
     note = {},
     url = {http://www.openphacts.org/specs/datadesc/},
     optannote = {}
   }
   
3. The Pharmacology Workspace: A Platform for Drug Discovery
   Gray, Alasdair J. G. and Askjaer, Sune and Brenninkmeijer, Christian Y. A. and Burger, Kees and Chichester, Christine and Eales, James M. and Evelo, Chris T. A. and Goble, Carole A. and Groth, Paul T. and Harland, Lee and Loizou, Antonis and Pettifer, Steve and Ramgolam, Rishi and Thompson, Mark and Waagmeester, Andra and Williams, Antony J.
   In Proceedings of the 3rd International Conference on Biomedical Ontology (ICBO 2012), KR-MED Series, Graz, Austria, July 21-25, 2012, CEUR Workshop Proceedings, 897, CEUR-WS.org, 2012
   

   @inproceedings{DBLP:conf/icbo/GrayABBCEEGGHLPRTWW12,
     author = {Gray, Alasdair J. G. and Askjaer, Sune and Brenninkmeijer, Christian Y. A. and Burger, Kees and Chichester, Christine and Eales, James M. and Evelo, Chris T. A. and Goble, Carole A. and Groth, Paul T. and Harland, Lee and Loizou, Antonis and Pettifer, Steve and Ramgolam, Rishi and Thompson, Mark and Waagmeester, Andra and Williams, Antony J.},
     title = {The Pharmacology Workspace: {A} Platform for Drug Discovery},
     booktitle = {Proceedings of the 3rd International Conference on Biomedical Ontology
                      {(ICBO} 2012), {KR-MED} Series, Graz, Austria, July 21-25, 2012},
     series = {{CEUR} Workshop Proceedings},
     volume = {897},
     publisher = {CEUR-WS.org},
     month = jul,
     year = {2012},
     url = {http://ceur-ws.org/Vol-897/demo\_4.pdf}
   }
   
4. The Pharmacology Workspace: A Platform for Drug Discovery
   Gray, A.J.G. and Askjaer, S. and Brenninkmeijer, C.Y. and Burger, K. and Chichester, C. and Eales, J. and Evelo, C.T. and Goble, C. and Groth, P. and Harland, L. and Loizou, A. and Pettifer, S. and Ramgolam, R. and Thompson, M. and Waagmeester, A. and Williams, A.J.
   In 3rd International Conference on Biomedical Ontology (ICBO 2012), Graz, Austria, 2012
   (Demo Paper)
   

   We present the Open PHACTS linked data platform that is being developed to address a set of example drug discovery research questions and which supports several drug discovery applications. The platform retrieves data from many complementary, but overlapping, data sources to present an integrated view of the data. The platform exploits two entity resolution services: respectively for transforming text and chemical structures to a concept. The single concept URI provided by the resolution service is then expanded to a set of equivalent URIs used by the data sources. Availability. An alpha version is currently available to the Open PHACTS consortium. A first public release of the platform will be made in late 2012, see http://www.openphacts.org/.

   @inproceedings{Gray:2012The-Pharmacology-Workspace:-A-Platform-for-Drug,
     address = {Graz, Austria},
     author = {Gray, A.J.G. and Askjaer, S. and Brenninkmeijer, C.Y. and Burger, K. and Chichester, C. and Eales, J. and Evelo, C.T. and Goble, C. and Groth, P. and Harland, L. and Loizou, A. and Pettifer, S. and Ramgolam, R. and Thompson, M. and Waagmeester, A. and Williams, A.J.},
     booktitle = {3rd International Conference on Biomedical Ontology (ICBO 2012)},
     month = jul,
     note = {(Demo Paper)},
     title = {The Pharmacology Workspace: A Platform for Drug Discovery},
     webpdf = {http://kr-med.org/icbofois2012/proceedings/ICBO2012/ICBO2012DemosSingleFiles/ICBO-2012-session6-Gray.pdf},
     year = {2012}
   }
   
5. Query Strategies to Support Context-Specific Views Through Stand-off Data Mappings
   Brenninkmeijer, C.Y.A. and Goble, C. and Gray, A.J.G. and Groth, P. and Loizou, A. and Pettifer, S.
   Technical Report. University of Manchester. 2012
   (Alphabetic authorship)
   

   @techreport{query-expansion,
     author = {Brenninkmeijer, C.Y.A. and Goble, C. and Gray, A.J.G. and Groth, P. and Loizou, A. and Pettifer, S.},
     title = {Query Strategies to Support Context-Specific Views Through Stand-off Data Mappings},
     institution = {University of Manchester},
     year = {2012},
     optkey = {},
     opttype = {},
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     optannote = {}
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2011

1. Spatial Information Management Application: Semantic Sensor Webs for Coastal Flooding
   Watt, Sam and Newman, Robin and Hutton, Craig and Sadler, Jason and Gray, Alasdair J. G.
   In Coast GIS 2011, Oostende, Belgium, 2011
   (Extended abstract)
   

   @inproceedings{Sadler2011-Spatial-,
     author = {Watt, Sam and Newman, Robin and Hutton, Craig and Sadler, Jason and Gray, Alasdair J. G.},
     title = {Spatial Information Management Application: Semantic Sensor Webs for Coastal Flooding},
     booktitle = {Coast GIS 2011},
     year = {2011},
     address = {Oostende, Belgium},
     month = sep,
     note = {(Extended abstract)},
     url = {http://coastgis.corila.it/2011/download/abstract/TC-025_Watt_et_al_abstract.pdf}
   }
   
2. Advances in Databases, 28th British National Conference on Databases
   Fernandes, Alvaro A. A. and Gray, Alasdair J. G. and Belhajjame, Khalid
   Lecture Notes in Computer Science, 7051, Springer, 2011
   ISBN: 978-3-642-24576-3
   

   @proceedings{bncod2011,
     address = {Manchester, UK},
     booktitle = {BNCOD},
     editor = {Fernandes, Alvaro A. A. and Gray, Alasdair J. G. and Belhajjame, Khalid},
     month = jul,
     publisher = {Springer},
     series = {Lecture Notes in Computer Science},
     title = {Advances in Databases, 28th British National Conference on Databases},
     volume = {7051},
     year = {2011},
     doi = {10.1007/978-3-642-24577-0},
     isbn = {978-3-642-24576-3}
   }
   
3. Executing in-network queries using SNEE
   Galpin, I. and Taylor, R. and Gray, A.J.G. and Brenninkmeijer, C.Y.A. and Fernandes, A.A.A. and Paton, N.W.
   In 28th British National Conference on Databases (BNCOD 2011), Manchester, UK, Lecture Notes in Computer Science, 7051, pages 136-139, Springer, 2011
   (Demo Paper)
   

   The SNEE query optimizer enables users to characterize data requests against wireless sensor networks (WSNs), using a declarative query language called SNEEql (SNEE for Sensor NEtwork Engine, described in [GBG+11], and publicly available at http://code.google.com/p/snee ). Queries are compiled into imperative query execution plans, which are translated into executable nesC source code. In this paper, we illustrate the lifecycle of a SNEEql query Q for in-network execution. This lifecycle encompasses the steps of preparatory metadata collection, followed by the compilation of Q into a query execution plan QEP, the dissemination of binary images implementing QEP throughout the WSN, and the generation of query results.

   @inproceedings{Galpin-etal:SNEE-OTA-DEMO:BNCOD2011,
     address = {Manchester, UK},
     author = {Galpin, I. and Taylor, R. and Gray, A.J.G. and Brenninkmeijer, C.Y.A. and Fernandes, A.A.A. and Paton, N.W.},
     booktitle = {28th British National Conference on Databases (BNCOD 2011)},
     doi = {10.1007/978-3-642-24577-0_15},
     month = jul,
     note = {(Demo Paper)},
     pages = {136-139},
     publisher = {Springer},
     series = {Lecture Notes in Computer Science},
     title = {Executing in-network queries using {SNEE}},
     volume = {7051},
     year = {2011},
     url = {https://doi.org/10.1007/978-3-642-24577-0_15}
   }
   
4. Extending query languages for in-network query processing
   Valkanas, G. and Gunopulos, D. and Galpin, I. and Gray, A.J.G. and Fernandes:, A.A.A.
   In 10th ACM International Workshop on Data Engineering for Wireless and Mobile Access (MobiDE 2011), Athens, Greece, pages 34-41, ACM, 2011
   

   Sensor networks have become ubiquitous and their proliferation in day-to-day life provides new research challenges. Sensors deployed at forest sites, high performance facilities, or areas striken by environmental, or other, phenomena, are only a few representative examples. More recently, mobile sensor networks have made their presence and are rapidly growing in numbers, such as the successful ZebraNet project or PDAs and smartphones. Nevertheless, such networks have mainly been used for data acquisition and data are being processed externally instead of in-network. Basic research problems that arise in the in-network setting include how to adjust in a timely and efficient manner to changing conditions and network topology. In this paper, we present a methodology, based on declarative query processing to alleviate the aforementioned problems, by making the deployment and optimization of a data analysis application as automatic as possible, which also helps execution in mobile environments. Our proposed solution focuses on extending a state-of-the-art sensor network platform, SNEE, with builtin data analysis capabilities.

   @inproceedings{Valkanas:SNEE-A:MobiDE2011,
     author = {Valkanas, G. and Gunopulos, D. and Galpin, I. and Gray, A.J.G. and Fernandes:, A.A.A.},
     title = {Extending query languages for in-network query processing},
     booktitle = {10th ACM International Workshop on Data Engineering for Wireless and Mobile Access (MobiDE 2011)},
     year = {2011},
     pages = {34-41},
     month = jun,
     address = {Athens, Greece},
     publisher = {ACM},
     doi = {10.1145/1999309.1999318}
   }
   
5. Deploying in-network data analysis techniques in sensor networks
   Valkanas, George and Kotsifakos, Alexios and Gunopulos, Dimitrios and Galpin, Ixent and Gray, Alasdair J. G. and Fernandes, Alvaro A. A. and Paton, Norman W.
   In 12th IEEE International Conference on Mobile Data Management, MDM 2011, Luleå, Sweden, June 6-9, 2011, Volume 1, Luleå, Sweden, Lecture Notes in Computer Science, 6644, pages 300–314, Springer, 2011
   (Demo Paper)
   

   Sensor Networks have received considerable attention recently, as they provide manifold benefits. Not only are they a means for data acquisition and monitoring of unexplored or inaccessible areas, they are also a low-cost alternative for sensing the environment, which greatly aids to better understand our surroundings. A major motivation in either occasion is to acknowledge endangering situations and take action(s) accordingly. To this end, we would like to enable data mining or analysis techniques on top or, even better, within such networks, due to the prohibitive cost of communication in this setting. In this work, we demonstrate running data mining algorithms on a set of sensors, which are of low-processing power. In addition to showcasing the execution of data analysis algorithms on resource-constrained hardware, our demo is intended to show how to take advantage of the properties of each algorithm to make better use of the sensors and their capabilities. We support the execution and monitoring of these algorithms with a graphical user interface (GUI).

   @inproceedings{Valkanas-etal:DAT-SNEE-Demo:MDM2011,
     address = {Lule\aa, Sweden},
     author = {Valkanas, George and Kotsifakos, Alexios and Gunopulos, Dimitrios and Galpin, Ixent and Gray, Alasdair J. G. and Fernandes, Alvaro A. A. and Paton, Norman W.},
     booktitle = {12th {IEEE} International Conference on Mobile Data Management, {MDM}
     	2011, Lule{\aa}, Sweden, June 6-9, 2011, Volume 1},
     doi = {10.1109/MDM.2011.54},
     month = jun,
     note = {(Demo Paper)},
     series = {Lecture Notes in Computer Science},
     volume = {6644},
     pages = {300--314},
     publisher = {Springer},
     year = {2011},
     title = {Deploying in-network data analysis techniques in sensor networks},
     url = {https://doi.org/10.1109/MDM.2011.54}
   }
   
6. A Semantically Enabled Service Architecture for Mashups over Streaming and Stored Data
   Gray, Alasdair J. G. and Garcia-Castro, Raul and Kyzirakos, Kostis and Karpathiotakis, Manos and Calbimonte, Jean-Paul and Page, Kevin R. and Sadler, Jason and Frazer, Alex and Galpin, Ixent and Fernandes, Alvaro A. A. and Paton, Norman W. and Óscar Corcho and Koubarakis, Manolis and Roure, David De and Martinez, Kirk and Gómez-Pérez, Asunción
   In The Semanic Web: Research and Applications - 8th Extended Semantic Web Conference, ESWC 2011, Heraklion, Crete, Greece, May 29 - June 2, 2011, Proceedings, Part II, 2011
   

   Sensing devices are increasingly being deployed to monitor the physical world around us. One class of application for which sensor data is pertinent is environmental decision support systems, e.g. flood emergency response. However, in order to interpret the readings from the sensors, the data needs to be put in context through correlation with other sensor readings, sensor data histories, and stored data, as well as juxtaposing with maps and forecast models. In this paper we use a flood emergency response planning application to identify requirements for a semantic sensor web. We propose a generic service architecture to satisfy the requirements that uses semantic annotations to support well-informed interactions between the services. We present the SemSorGrid4Env realisation of the architecture and illustrate its capabilities in the context of the example application.

   @inproceedings{DBLP:conf/esws/GrayGKKCPSFGFPCKRMG11,
     author = {Gray, Alasdair J. G. and Garcia{-}Castro, Raul and Kyzirakos, Kostis and Karpathiotakis, Manos and Calbimonte, Jean-Paul and Page, Kevin R. and Sadler, Jason and Frazer, Alex and Galpin, Ixent and Fernandes, Alvaro A. A. and Paton, Norman W. and {\'{O}}scar Corcho and Koubarakis, Manolis and Roure, David De and Martinez, Kirk and G{\'{o}}mez{-}P{\'{e}}rez, Asunci{\'{o}}n},
     title = {A Semantically Enabled Service Architecture for Mashups over Streaming
                    and Stored Data},
     booktitle = {The Semanic Web: Research and Applications - 8th Extended Semantic
                    Web Conference, {ESWC} 2011, Heraklion, Crete, Greece, May 29 - June
                    2, 2011, Proceedings, Part {II}},
     year = {2011},
     month = may,
     url = {https://doi.org/10.1007/978-3-642-21064-8\_21},
     doi = {10.1007/978-3-642-21064-8\_21}
   }
   
7. Building Semantic Sensor Webs and Applications
   Corcho, O. and Gray, A.J.G. and Kyzirakos, K. and Calbimonte, J.-P. and Page, K.
   In European Semantic Web Conference (ESWC 2011) – Tutorial, 2011
   (Tutorial)
   

   @inproceedings{Corcho2011Building-Semant,
     author = {Corcho, O. and Gray, A.J.G. and Kyzirakos, K. and Calbimonte, J.-P. and Page, K.},
     booktitle = {European Semantic Web Conference (ESWC 2011) -- Tutorial},
     month = may,
     note = {(Tutorial)},
     title = {Building Semantic Sensor Webs and Applications},
     year = {2011}
   }
   
8. SNEE: a query processor for wireless sensor networks
   Galpin, Ixent and Brenninkmeijer, Christian Y. A. and Gray, Alasdair J. G. and Jabeen, Farhana and Fernandes, Alvaro A. A. and Paton, Norman W.
   Distributed and Parallel Databases, 29(1-2):31–85, 2011
   

   A wireless sensor network (WSN) can be construed as an intelligent, large-scale device for observing and measuring properties of the physical world. In recent years, the database research community has championed the view that if we construe a WSN as a database (i.e., if a significant aspect of its intelligent behavior is that it can execute declaratively-expressed queries), then one can achieve a significant reduction in the cost of engineering the software that implements a data collection program for the WSN while still achieving, through query optimization, very favorable cost:benefit ratios. This paper describes a query processing framework for WSNs that meets many desiderata associated with the view of WSN as databases. The framework is presented in the form of compiler/optimizer, called SNEE, for a continuous declarative query language over sensed data streams, called SNEEql. SNEEql can be shown to meet the expressiveness requirements of a large class of applications. SNEE can be shown to generate effective and efficient query evaluation plans. More specifically, the paper describes the following contributions: (1) a user-level syntax and physical algebra for SNEEql, an expressive continuous query language over WSNs; (2) example concrete algorithms for physical algebraic operators defined in such a way that the task of deriving memory, time and energy analytical cost-estimation models (CEMs) for them becomes straightforward by reduction to a structural traversal of the pseudocode; (3) CEMs for the concrete algorithms alluded to; (4) an architecture for the optimization of SNEEql queries, called SNEE, building on well-established distributed query processing components where possible, but making enhancements or refinements where necessary to accommodate the WSN context; (5) algorithms that instantiate the components in the SNEE architecture, thereby supporting integrated query planning that includes routing, placement and timing; and (6) an empirical performance evaluation of the resulting framework.

   @article{DBLP:journals/dpd/GalpinBGJFP11,
     author = {Galpin, Ixent and Brenninkmeijer, Christian Y. A. and Gray, Alasdair J. G. and Jabeen, Farhana and Fernandes, Alvaro A. A. and Paton, Norman W.},
     title = {{SNEE:} a query processor for wireless sensor networks},
     journal = {Distributed and Parallel Databases},
     volume = {29},
     number = {1-2},
     pages = {31--85},
     year = {2011},
     url = {https://doi.org/10.1007/s10619-010-7074-3},
     doi = {10.1007/s10619-010-7074-3}
   }
   
9. A Semantic Sensor Web for Environmental Decision Support Applications
   Gray, Alasdair J. G. and Sadler, Jason and Kit, Oles and Kyzirakos, Kostis and Karpathiotakis, Manos and Calbimonte, Jean-Paul and Page, Kevin R. and Garcı́a-Castro, Raúl and Frazer, Alex and Galpin, Ixent and Fernandes, Alvaro A. A. and Paton, Norman W. and Óscar Corcho and Koubarakis, Manolis and Roure, David De and Martinez, Kirk and Gómez-Pérez, Asunción
   Sensors, 11(9):8855–8887, 2011
   

   @article{DBLP:journals/sensors/GraySKKKCPGFGFP11,
     author = {Gray, Alasdair J. G. and Sadler, Jason and Kit, Oles and Kyzirakos, Kostis and Karpathiotakis, Manos and Calbimonte, Jean-Paul and Page, Kevin R. and Garc{\'{\i}}a{-}Castro, Ra{\'{u}}l and Frazer, Alex and Galpin, Ixent and Fernandes, Alvaro A. A. and Paton, Norman W. and {\'{O}}scar Corcho and Koubarakis, Manolis and Roure, David De and Martinez, Kirk and G{\'{o}}mez{-}P{\'{e}}rez, Asunci{\'{o}}n},
     title = {A Semantic Sensor Web for Environmental Decision Support Applications},
     journal = {Sensors},
     volume = {11},
     number = {9},
     pages = {8855--8887},
     year = {2011},
     url = {https://doi.org/10.3390/s110908855},
     doi = {10.3390/s110908855}
   }
   

2010

1. Enabling Ontology-Based Access to Streaming Data Sources
   Calbimonte, Jean-Paul and Óscar Corcho and Gray, Alasdair J. G.
   In The Semantic Web - ISWC 2010 - 9th International Semantic Web Conference, ISWC 2010, Shanghai, China, November 7-11, 2010, Revised Selected Papers, Part I, Lecture Notes in Computer Science, 6496, pages 96–111, Springer, 2010
   (Alphabetical authorship, equal responsibility)
   

   @inproceedings{DBLP:conf/semweb/CalbimonteCG10,
     author = {Calbimonte, Jean-Paul and {\'{O}}scar Corcho and Gray, Alasdair J. G.},
     title = {Enabling Ontology-Based Access to Streaming Data Sources},
     booktitle = {The Semantic Web - {ISWC} 2010 - 9th International Semantic Web Conference,
                    {ISWC} 2010, Shanghai, China, November 7-11, 2010, Revised Selected
                    Papers, Part {I}},
     series = {Lecture Notes in Computer Science},
     volume = {6496},
     pages = {96--111},
     publisher = {Springer},
     month = nov,
     note = {(Alphabetical authorship, equal responsibility)},
     year = {2010},
     url = {https://doi.org/10.1007/978-3-642-17746-0\_7},
     doi = {10.1007/978-3-642-17746-0\_7}
   }
   
2. Whither BNCOD? The Future of Database and Information Systems Research
   Gray, Alasdair J. G.
   In Data Security and Security Data - 27th British National Conference on Databases, BNCOD 27, Dundee, UK, June 29 - July 1, 2010. Revised Selected Papers, Dundee, UK, Lecture Notes in Computer Science, 6121, pages 3–6, Springer, 2010
   (Panel paper)
   

   @inproceedings{Gray2010Whither-BNCOD-T,
     address = {Dundee, UK},
     author = {Gray, Alasdair J. G.},
     booktitle = {Data Security and Security Data - 27th British National Conference on Databases, {BNCOD} 27, Dundee, UK, June 29 - July 1, 2010. Revised Selected Papers},
     doi = {10.1007/978-3-642-25704-9\_2},
     month = jul,
     note = {(Panel paper)},
     pages = {3--6},
     publisher = {Springer},
     series = {Lecture Notes in Computer Science},
     title = {Whither {BNCOD}? The Future of Database and Information Systems Research},
     url = {https://doi.org/10.1007/978-3-642-25704-9\_2},
     volume = {6121},
     year = {2010}
   }
   
3. Collaborative Editing and Linking of Astronomy Vocabularies Using Semantic Mediawiki
   Chalmers, Stuart and Gray, Norman and Ounis, Iadh and Gray, Alasdair J. G.
   In Proceedings of the 5th Workshop on Semantic Wikis, Hersonissos, Heraklion, Crete, Greece, May 31st, 2010, CEUR Workshop Proceedings, 632, CEUR-WS.org, 2010
   

   @inproceedings{DBLP:conf/semwiki/ChalmersGOG10,
     author = {Chalmers, Stuart and Gray, Norman and Ounis, Iadh and Gray, Alasdair J. G.},
     title = {Collaborative Editing and Linking of Astronomy Vocabularies Using
                    Semantic Mediawiki},
     booktitle = {Proceedings of the 5th Workshop on Semantic Wikis, Hersonissos, Heraklion,
                    Crete, Greece, May 31st, 2010},
     series = {{CEUR} Workshop Proceedings},
     volume = {632},
     publisher = {CEUR-WS.org},
     month = may,
     year = {2010},
     url = {http://ceur-ws.org/Vol-632/paper06.pdf}
   }
   
4. Distributed Query Processing over Streaming and Stored Data
   Gray, A. J. G.
   In Workshop on Semantic Challenges in Sensor Networks, Dagstuhl, Germany, 10042, 2010
   

   @inproceedings{Gray2010DQPDagstuhl,
     author = {Gray, A. J. G.},
     title = {Distributed Query Processing over Streaming and Stored Data},
     optcrossref = {},
     optkey = {},
     booktitle = {Workshop on Semantic Challenges in Sensor Networks},
     optpages = {},
     year = {2010},
     opteditor = {},
     volume = {10042},
     optnumber = {},
     optseries = {},
     address = {Dagstuhl, Germany},
     month = jan,
     optorganization = {},
     optpublisher = {},
     url = {https://www.dagstuhl.de/10042},
     optnote = {},
     optannote = {}
   }
   
5. SNEE In-WSN Query Processing Demonstration
   Gray, A. J. G.
   In Workshop on Semantic Challenges in Sensor Networks, Dagstuhl, Germany, 10042, 2010
   

   @inproceedings{Gray2010SNEEDemo,
     author = {Gray, A. J. G.},
     title = {{SNEE} {In-WSN} Query Processing Demonstration},
     optcrossref = {},
     optkey = {},
     booktitle = {Workshop on Semantic Challenges in Sensor Networks},
     optpages = {},
     year = {2010},
     opteditor = {},
     volume = {10042},
     optnumber = {},
     optseries = {},
     address = {Dagstuhl, Germany},
     month = jan,
     optorganization = {},
     optpublisher = {},
     url = {https://www.dagstuhl.de/10042},
     optnote = {},
     optannote = {}
   }
   
6. Finding the right term: Retrieving and exploring semantic concepts in astronomical vocabularies
   Gray, Alasdair J. G. and Gray, Norman and Hall, Christopher W. and Ounis, Iadh
   Information Processing and Management, 46(4):470–478, 2010
   (Alphabetic authorship)
   

   Astronomy, like many domains, already has several sets of terminology in general use, referred to as controlled vocabularies. For example, the keywords for tagging journal articles, or the taxonomy of terms used to label image files. These existing vocabularies can be encoded into skos, a W3C proposed recommendation for representing vocabularies on the Semantic Web, so that computer systems can help users to search for and discover resources tagged with vocabulary concepts. However, this requires a search mechanism to go from a user-supplied string to a vocabulary concept. In this paper, we present our experiences in implementing the Vocabulary Explorer, a vocabulary search service based on the Terrier Information Retrieval Platform. We investigate the capabilities of existing document weighting models for identifying the correct vocabulary concept for a query. Due to the highly structured nature of a skos encoded vocabulary, we investigate the effects of term weighting (boosting the score of concepts that match on particular fields of a vocabulary concept), and query expansion. We found that the existing document weighting models provided very high quality results, but these could be improved further with the use of term weighting that makes use of the semantic evidence.

   @article{DBLP:journals/ipm/GrayGHO10,
     author = {Gray, Alasdair J. G. and Gray, Norman and Hall, Christopher W. and Ounis, Iadh},
     title = {Finding the right term: Retrieving and exploring semantic concepts
                    in astronomical vocabularies},
     journal = {Information Processing and Management},
     volume = {46},
     number = {4},
     pages = {470--478},
     year = {2010},
     note = {(Alphabetic authorship)},
     url = {https://doi.org/10.1016/j.ipm.2009.09.004},
     doi = {10.1016/j.ipm.2009.09.004}
   }
   

2009

1. Can RDB2RDF Tools Feasibily Expose Large Science Archives for Data Integration?
   Gray, Alasdair J. G. and Gray, Norman and Ounis, Iadh
   In The Semantic Web: Research and Applications, 6th European Semantic Web Conference, ESWC 2009, Heraklion, Crete, Greece, May 31-June 4, 2009, Proceedings, Lecture Notes in Computer Science, 5554, pages 491–505, Springer, 2009
   

   @inproceedings{DBLP:conf/esws/GrayGO09,
     author = {Gray, Alasdair J. G. and Gray, Norman and Ounis, Iadh},
     title = {Can {RDB2RDF} Tools Feasibily Expose Large Science Archives for Data
                    Integration?},
     booktitle = {The Semantic Web: Research and Applications, 6th European Semantic
                    Web Conference, {ESWC} 2009, Heraklion, Crete, Greece, May 31-June
                    4, 2009, Proceedings},
     series = {Lecture Notes in Computer Science},
     volume = {5554},
     pages = {491--505},
     publisher = {Springer},
     month = jun,
     year = {2009},
     url = {https://doi.org/10.1007/978-3-642-02121-3\_37},
     doi = {10.1007/978-3-642-02121-3\_37}
   }
   
2. Searching and exploring controlled vocabularies
   Gray, A.J.G. and Gray, N. and Ounis, I.
   In Exploiting Semantic Annotations in Information Retrieval (ESAIR 2009), Barcelona, Spain, pages 1-5, 2009
   

   @inproceedings{Gray2009Searching-and-e,
     address = {Barcelona, Spain},
     author = {Gray, A.J.G. and Gray, N. and Ounis, I.},
     booktitle = {Exploiting Semantic Annotations in Information Retrieval (ESAIR 2009)},
     pages = {1-5},
     title = {Searching and exploring controlled vocabularies},
     year = {2009}
   }
   
3. Vocabularies in the Virtual Observatory
   Gray, A.J.G. and Gray, N. and Hessman, F.V. and Preite Martinez (Eds), A.
   Recommendation, v1.19. IVOA. 2009
   \urlhttp://www.ivoa.net/Documents/latest/Vocabularies.html
   

   @techreport{gray-etal:vocab-VO:2009,
     author = {Gray, A.J.G. and Gray, N. and Hessman, F.V. and {Preite Martinez (Eds)}, A.},
     institution = {IVOA},
     note = {\url{http://www.ivoa.net/Documents/latest/Vocabularies.html}},
     number = {v1.19},
     title = {Vocabularies in the Virtual Observatory},
     type = {Recommendation},
     year = {2009},
     url = {http://www.ivoa.net/Documents/latest/Vocabularies.html}
   }
   

2008

1. Vocabularies in the VO
   Gray, A.J.G. and Gray, N. and Ounis, I.
   In Astronomical Data Analysis Software and Systems (ADASS XVIII), Québec City, Canada, 411, Astronomical Society of the Pacific, 2008
   (Extended abstract)
   

   @inproceedings{Gray2008Vocabularies-in,
     address = {Qu{\'e}bec City, Canada},
     author = {Gray, A.J.G. and Gray, N. and Ounis, I.},
     booktitle = {Astronomical Data Analysis Software and Systems (ADASS XVIII)},
     page = {179},
     publisher = {Astronomical Society of the Pacific},
     title = {Vocabularies in the {VO}},
     volume = {411},
     month = nov,
     year = {2008},
     note = {(Extended abstract)}
   }
   
2. Finding Data Resources in a Virtual Observatory Using SKOS Vocabularies
   Gray, Alasdair J. G. and Gray, Norman and Ounis, Iadh
   In Sharing Data, Information and Knowledge, 25th British National Conference on Databases, BNCOD 25, Cardiff, UK, July 7-10, 2008. Proceedings, Cardiff, UK, Lecture Notes in Computer Science, 5071, pages 189–192, Springer, 2008
   (Poster paper)
   

   @inproceedings{Gray2008Finding-Data-Re,
     address = {Cardiff, UK},
     author = {Gray, Alasdair J. G. and Gray, Norman and Ounis, Iadh},
     booktitle = {Sharing Data, Information and Knowledge, 25th British National Conference on Databases, {BNCOD} 25, Cardiff, UK, July 7-10, 2008. Proceedings},
     doi = {10.1007/978-3-540-70504-8\_19},
     month = jul,
     note = {(Poster paper)},
     pages = {189--192},
     publisher = {Springer},
     series = {Lecture Notes in Computer Science},
     title = {Finding Data Resources in a Virtual Observatory Using {SKOS} Vocabularies},
     url = {https://doi.org/10.1007/978-3-540-70504-8\_19},
     volume = {5071},
     year = {2008}
   }
   
3. Accessing existing distributed science archives as RDF models
   Gray, A.J.G. and Gray, N. and Ounis, I.
   In UK e-Science All Hands Meeting, Edinburgh, UK, 2008
   

   @inproceedings{Gray2008Accessing-exist,
     address = {Edinburgh, UK},
     author = {Gray, A.J.G. and Gray, N. and Ounis, I.},
     booktitle = {UK e-Science All Hands Meeting},
     title = {Accessing existing distributed science archives as {RDF} models},
     year = {2008}
   }
   

2007

1. Answering queries over incomplete data stream histories
   Gray, Alasdair J. G. and Nutt, Werner and Williams, M. Howard
   International Journal of Web Information Systems (IJWIS), 3(1/2):41–60, 2007
   

   Purpose Distributed data streams are an important topic of current research. In such a setting, data values will be missed, e.g. due to network errors. This paper aims to allow this incompleteness to be detected and overcome with either the user not being affected or the effects of the incompleteness being reported to the user. Design/methodology/approach A model for representing the incomplete information has been developed that captures the information that is known about the missing data. Techniques for query answering involving certain and possible answer sets have been extended so that queries over incomplete data stream histories can be answered. Findings It is possible to detect when a distributed data stream is missing one or more values. When such data values are missing there will be some information that is known about the data and this is stored in an appropriate format. Even when the available data are incomplete, it is possible in some circumstances to answer a query completely. When this is not possible, additional meta‐data can be returned to inform the user of the effects of the incompleteness. Research limitations/implications The techniques and models proposed in this paper have only been partially implemented. Practical implications The proposed system is general and can be applied wherever there is a need to query the history of distributed data streams. The work in this paper enables the system to answer queries when there are missing values in the data. Originality/value This paper presents a general model of how to detect, represent, and answer historical queries over incomplete distributed data streams.

   @article{Gray:AnsQIncompleteStream:IJWIS2007,
     author = {Gray, Alasdair J. G. and Nutt, Werner and Williams, M. Howard},
     title = {Answering queries over incomplete data stream histories},
     journal = {International Journal of Web Information Systems ({IJWIS})},
     volume = {3},
     number = {1/2},
     pages = {41--60},
     year = {2007},
     url = {https://doi.org/10.1108/17440080710829216},
     doi = {10.1108/17440080710829216}
   }
   
2. Integrating Distributed Data Streams
   Gray, Alasdair J.G.
   PhD Thesis, Heriot-Watt University, Edinburgh, UK, 2007
   

   There is an increasing amount of information being made available as data streams, e.g. stock tickers, data from sensor networks, smart homes, monitoring data, etc. In many cases, this data is generated by distributed sources under the control of many different organisations. Users would like to seamlessly query such data without prior knowledge of where it is located or how it is published. This is similar to the problem of integrating data residing in multiple heterogeneous stored data sources. However, the techniques developed for stored data are not applicable due to the continuous and long-lived nature of queries over data streams. This thesis proposes an architecture for a stream integration system. A key feature of the architecture is a republisher component that collects together distributed streams and makes the merged stream available for querying. A formal model for the system has been developed and is used to generate plans for executing continuous queries which exploit the redundancy introduced by the republishers. Additionally, due to the long-lived nature of continuous queries, mechanisms for maintaining the plans whenever there is a change in the set of data sources have been developed. A prototype of the system has been implemented and performance measures made. The work of this thesis has been motivated by the problem of retrieving monitoring information about Grid resources. However, the techniques developed are general and can be applied wherever there is a need to publish and query distributed data involving data streams.

   @phdthesis{Gray2007Integrating-Dis,
     address = {Edinburgh, UK},
     author = {Gray, Alasdair J.G.},
     school = {Heriot-Watt University},
     title = {Integrating Distributed Data Streams},
     url = {http://AlasdairGray.github.io/publications/thesis-final_web-copy.pdf},
     year = {2007}
   }
   

2006

1. Answering Arbitrary Conjunctive Queries over Incomplete Data Stream Histories
   Gray, Alasdair J. G. and Williams, M. Howard and Nutt, Werner
   In iiWAS’2006 - The Eighth International Conference on Information Integration and Web-based Applications Services, 4-6 December 2006, Yogyakarta, Indonesia, books@ocg.at, 214, pages 259–268, Austrian Computer Society, 2006
   

   @inproceedings{DBLP:conf/iiwas/GrayWN06,
     author = {Gray, Alasdair J. G. and Williams, M. Howard and Nutt, Werner},
     title = {Answering Arbitrary Conjunctive Queries over Incomplete Data Stream
                    Histories},
     booktitle = {iiWAS'2006 - The Eighth International Conference on Information Integration
                    and Web-based Applications Services, 4-6 December 2006, Yogyakarta,
                    Indonesia},
     series = {books@ocg.at},
     volume = {214},
     pages = {259--268},
     publisher = {Austrian Computer Society},
     month = dec,
     year = {2006}
   }
   
2. Sources of Incompleteness in Grid Publishing
   Gray, Alasdair J. G. and Nutt, Werner and Williams, M. Howard
   In Flexible and Efficient Information Handling, 23rd British National Conference on Databases, BNCOD 23, Belfast, Northern Ireland, UK, July 18-20, 2006, Proceedings, Lecture Notes in Computer Science, 4042, pages 94–101, Springer, 2006
   

   @inproceedings{DBLP:conf/bncod/GrayNW06,
     author = {Gray, Alasdair J. G. and Nutt, Werner and Williams, M. Howard},
     title = {Sources of Incompleteness in Grid Publishing},
     booktitle = {Flexible and Efficient Information Handling, 23rd British National
                    Conference on Databases, {BNCOD} 23, Belfast, Northern Ireland, UK,
                    July 18-20, 2006, Proceedings},
     series = {Lecture Notes in Computer Science},
     volume = {4042},
     pages = {94--101},
     publisher = {Springer},
     month = jul,
     year = {2006},
     url = {https://doi.org/10.1007/11788911\_8},
     doi = {10.1007/11788911\_8}
   }
   

2005

1. A Data Stream Publish/Subscribe Architecture with Self-adapting Queries
   Gray, Alasdair J. G. and Nutt, Werner
   In On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and ODBASE, OTM Confederated International Conferences CoopIS, DOA, and ODBASE 2005, Agia Napa, Cyprus, October 31 - November 4, 2005, Proceedings, Part I, Lecture Notes in Computer Science, 3760, pages 420–438, Springer, 2005
   

   @inproceedings{DBLP:conf/otm/GrayN05,
     author = {Gray, Alasdair J. G. and Nutt, Werner},
     title = {A Data Stream Publish/Subscribe Architecture with Self-adapting Queries},
     booktitle = {On the Move to Meaningful Internet Systems 2005: CoopIS, DOA, and
                    ODBASE, {OTM} Confederated International Conferences CoopIS, DOA,
                    and {ODBASE} 2005, Agia Napa, Cyprus, October 31 - November 4, 2005,
                    Proceedings, Part {I}},
     series = {Lecture Notes in Computer Science},
     volume = {3760},
     pages = {420--438},
     publisher = {Springer},
     month = oct,
     year = {2005},
     url = {https://doi.org/10.1007/11575771\_27},
     doi = {10.1007/11575771\_27}
   }
   
2. Republishers in a Publish/Subscribe Architecture for Data Streams
   Gray, Alasdair J. G. and Nutt, Werner
   In Database: Enterprise, Skills and Innovation, 22nd British National Conference on Databases, BNCOD 22, Sunderland, UK, July 5-7, 2005, Proceedings, Lecture Notes in Computer Science, 3567, pages 179–184, Springer, 2005
   

   @inproceedings{DBLP:conf/bncod/GrayN05,
     author = {Gray, Alasdair J. G. and Nutt, Werner},
     title = {Republishers in a Publish/Subscribe Architecture for Data Streams},
     booktitle = {Database: Enterprise, Skills and Innovation, 22nd British National
                    Conference on Databases, {BNCOD} 22, Sunderland, UK, July 5-7, 2005,
                    Proceedings},
     series = {Lecture Notes in Computer Science},
     volume = {3567},
     pages = {179--184},
     publisher = {Springer},
     month = jul,
     year = {2005},
     url = {https://doi.org/10.1007/11511854\_17},
     doi = {10.1007/11511854\_17}
   }
   
3. Fault Tolerance in the R-GMA Information and Monitoring System
   Byrom, Rob and Coghlan, Brian A. and Cooke, Andrew W. and Cordenonsi, Roney and Cornwall, Linda and Craig, Martin and Djaoui, Abdeslem and Duncan, Alastair and Fisher, Steve and Gray, Alasdair J. G. and Hicks, Steve and Kenny, Stuart and Leake, Jason and Lyttleton, Oliver and Magowan, James and Middleton, Robin and Nutt, Werner and O’Callaghan, David and Podhorszki, Norbert and Taylor, Paul and Walk, John and Wilson, Antony J.
   In Advances in Grid Computing - EGC 2005, European Grid Conference, Amsterdam, The Netherlands, February 14-16, 2005, Revised Selected Papers, Lecture Notes in Computer Science, 3470, pages 751–760, Springer, 2005
   (Alphabetical authorship)
   

   @inproceedings{DBLP:conf/egc/ByromCCCCCDDFGHKLLMMNOPTWW05,
     author = {Byrom, Rob and Coghlan, Brian A. and Cooke, Andrew W. and Cordenonsi, Roney and Cornwall, Linda and Craig, Martin and Djaoui, Abdeslem and Duncan, Alastair and Fisher, Steve and Gray, Alasdair J. G. and Hicks, Steve and Kenny, Stuart and Leake, Jason and Lyttleton, Oliver and Magowan, James and Middleton, Robin and Nutt, Werner and O'Callaghan, David and Podhorszki, Norbert and Taylor, Paul and Walk, John and Wilson, Antony J.},
     title = {Fault Tolerance in the {R-GMA} Information and Monitoring System},
     booktitle = {Advances in Grid Computing - {EGC} 2005, European Grid Conference,
                    Amsterdam, The Netherlands, February 14-16, 2005, Revised Selected
                    Papers},
     series = {Lecture Notes in Computer Science},
     volume = {3470},
     pages = {751--760},
     publisher = {Springer},
     month = feb,
     year = {2005},
     note = {(Alphabetical authorship)},
     url = {https://doi.org/10.1007/11508380\_76},
     doi = {10.1007/11508380\_76}
   }
   
4. Stream Integration Techniques for Grid Monitoring
   Cooke, Andrew W. and Gray, Alasdair J. G. and Nutt, Werner
   Journal on Data Semantics, 2:136–175, 2005
   (Alphabetical authorship, equal responsibility)
   

   @article{Cooke:StreamIntegration:JoDS2005,
     author = {Cooke, Andrew W. and Gray, Alasdair J. G. and Nutt, Werner},
     title = {Stream Integration Techniques for Grid Monitoring},
     journal = {Journal on Data Semantics},
     volume = {2},
     pages = {136--175},
     year = {2005},
     note = {(Alphabetical authorship, equal responsibility)},
     url = {https://doi.org/10.1007/978-3-540-30567-5\_6},
     doi = {10.1007/978-3-540-30567-5\_6}
   }
   

2004

1. Answering continuous queries using views
   Gray, A.J.G. and Nutt, W.
   In 5th Postgraduate Research Conference in Electronics, Photonics, Communications and Networks, and Computing Science (PREP 2004), Hatfield, UK, 2004
   (Poster paper)
   

   @inproceedings{Gray2004ACQUV,
     address = {Hatfield, UK},
     author = {Gray, A.J.G. and Nutt, W.},
     booktitle = {5th Postgraduate Research Conference in Electronics, Photonics, Communications and Networks, and Computing Science (PREP 2004)},
     month = apr,
     note = {(Poster paper)},
     title = {Answering continuous queries using views},
     year = {2004}
   }
   
2. Planning continuous selection queries using views
   Gray, A. J. G. and Cooke, A. and Nutt, W.
   In Workshop on Logic Based Information Agents, Dagstuhl, Germany, 04171, 2004
   

   @inproceedings{Gray2004Planning-cont,
     author = {Gray, A. J. G. and Cooke, A. and Nutt, W.},
     title = {Planning continuous selection queries using views},
     optcrossref = {},
     optkey = {},
     booktitle = {Workshop on Logic Based Information Agents},
     optpages = {},
     year = {2004},
     opteditor = {},
     volume = {04171},
     optnumber = {},
     optseries = {},
     address = {Dagstuhl, Germany},
     month = apr,
     optorganization = {},
     optpublisher = {},
     url = {https://www.dagstuhl.de/en/program/calendar/semhp/?semnr=04171},
     optnote = {},
     optannote = {}
   }
   
3. The Relational Grid Monitoring Architecture: Mediating Information about the Grid
   Cooke, Andrew W. and Gray, Alasdair J. G. and Nutt, Werner and Magowan, James and Oevers, Manfred and Taylor, Paul and Cordenonsi, Roney and Byrom, Rob and Cornwall, Linda and Djaoui, Abdeslem and Field, Laurence and Fisher, Steve and Hicks, Steve and Leake, Jason and Middleton, Robin and Wilson, Antony J. and Zhu, Xiaomei and Podhorszki, Norbert and Coghlan, Brian A. and Kenny, Stuart and O’Callaghan, David and Ryan, John
   Journal of Grid Computing, 2(4):323–339, 2004
   (Alphabetical authorship by site, Heriot-Watt authored paper)
   

   We have developed and implemented the Relational Grid Monitoring Architecture (R-GMA) as part of the DataGrid project, to provide a flexible information and monitoring service for use by other middleware components and applications. R-GMA presents users with a virtual database and mediates queries posed at this database: users pose queries against a global schema and R-GMA takes responsibility for locating relevant sources and returning an answer. R-GMA’s architecture and mechanisms are general and can be used wherever there is a need for publishing and querying information in a distributed environment. We discuss the requirements, design and implementation of R-GMA as deployed on the DataGrid testbed. We also describe some of the ways in which R-GMA is being used.

   @article{Cooke:RGMA:JoGC2004,
     author = {Cooke, Andrew W. and Gray, Alasdair J. G. and Nutt, Werner and Magowan, James and Oevers, Manfred and Taylor, Paul and Cordenonsi, Roney and Byrom, Rob and Cornwall, Linda and Djaoui, Abdeslem and Field, Laurence and Fisher, Steve and Hicks, Steve and Leake, Jason and Middleton, Robin and Wilson, Antony J. and Zhu, Xiaomei and Podhorszki, Norbert and Coghlan, Brian A. and Kenny, Stuart and O'Callaghan, David and Ryan, John},
     title = {The Relational Grid Monitoring Architecture: Mediating Information
                    about the Grid},
     journal = {Journal of Grid Computing},
     volume = {2},
     number = {4},
     pages = {323--339},
     year = {2004},
     note = {(Alphabetical authorship by site, Heriot-Watt authored paper)},
     url = {https://doi.org/10.1007/s10723-005-0151-6},
     doi = {10.1007/s10723-005-0151-6}
   }
   
4. Production services for information and monitoring in the grid
   Byrom, Rob and Coghlan, Brian and Cooke, Andy and Cordenonsi, Roney and Cornwall, Linda and Craig, Martin and Djaoui, Abdeslem and Fisher, Steve and Gray, Alasdair and Hicks, Steve and others
   In AHM2004, Nottingham, UK, 2004
   

   @inproceedings{byrom2004production,
     title = {Production services for information and monitoring in the grid},
     author = {Byrom, Rob and Coghlan, Brian and Cooke, Andy and Cordenonsi, Roney and Cornwall, Linda and Craig, Martin and Djaoui, Abdeslem and Fisher, Steve and Gray, Alasdair and Hicks, Steve and others},
     booktitle = {AHM2004, Nottingham, UK},
     year = {2004}
   }
   

2003

1. R-GMA: An Information Integration System for Grid Monitoring
   Cooke, Andrew W. and Gray, Alasdair J. G. and Ma, Lisha and Nutt, Werner and Magowan, James and Oevers, Manfred and Taylor, Paul and Byrom, Rob and Field, Laurence and Hicks, Steve and Leake, Jason and Soni, Manish and Wilson, Antony J. and Cordenonsi, Roney and Cornwall, Linda and Djaoui, Abdeslem and Fisher, Steve and Podhorszki, Norbert and Coghlan, Brian A. and Kenny, Stuart and O’Callaghan, David
   In On The Move to Meaningful Internet Systems 2003: CoopIS, DOA, and ODBASE - OTM Confederated International Conferences, CoopIS, DOA, and ODBASE 2003, Catania, Sicily, Italy, November 3-7, 2003, Lecture Notes in Computer Science, 2888, pages 462–481, Springer, 2003
   

   @inproceedings{Cooke:RGMA:CoopIS2003,
     author = {Cooke, Andrew W. and Gray, Alasdair J. G. and Ma, Lisha and Nutt, Werner and Magowan, James and Oevers, Manfred and Taylor, Paul and Byrom, Rob and Field, Laurence and Hicks, Steve and Leake, Jason and Soni, Manish and Wilson, Antony J. and Cordenonsi, Roney and Cornwall, Linda and Djaoui, Abdeslem and Fisher, Steve and Podhorszki, Norbert and Coghlan, Brian A. and Kenny, Stuart and O'Callaghan, David},
     title = {{R-GMA:} An Information Integration System for Grid Monitoring},
     booktitle = {On The Move to Meaningful Internet Systems 2003: CoopIS, DOA, and
                    {ODBASE} - {OTM} Confederated International Conferences, CoopIS, DOA,
                    and {ODBASE} 2003, Catania, Sicily, Italy, November 3-7, 2003},
     series = {Lecture Notes in Computer Science},
     volume = {2888},
     pages = {462--481},
     publisher = {Springer},
     month = nov,
     year = {2003},
     url = {https://doi.org/10.1007/978-3-540-39964-3\_29},
     doi = {10.1007/978-3-540-39964-3\_29}
   }
   

About Me

I'm an Associate Professor in Computer Science at Heriot-Watt University. My research focuses on linking datasets. Read more

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