@article{Hasnain2017,
author = {Hasnain, Ali and Mehmood, Qaiser and {Sana e Zainab}, Syeda and Saleem, Muhammad and Warren, Claude and Zehra, Durre and Decker, Stefan and Rebholz-Schuhmann, Dietrich},
doi = {10.1186/s13326-017-0118-0},
issn = {2041-1480},
journal = {Journal of Biomedical Semantics},
mendeley-groups = {LECA},
month = {dec},
number = {1},
pages = {13},
title = {{BioFed: federated query processing over life sciences linked open data}},
url = {http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0118-0},
volume = {8},
year = {2017}
}
@article{Coissac2016,
author = {Coissac, Eric and Hollingsworth, Peter M. and Lavergne, S{\'{e}}bastien and Taberlet, Pierre},
doi = {10.1111/mec.13549},
issn = {09621083},
journal = {Molecular Ecology},
month = {apr},
number = {7},
pages = {1423--1428},
title = {{From barcodes to genomes: extending the concept of DNA barcoding}},
url = {http://doi.wiley.com/10.1111/mec.13549},
volume = {25},
year = {2016}
}
@article{Bandrowski2016,
abstract = {The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.},
author = {Bandrowski, Anita and Brinkman, Ryan and Brochhausen, Mathias and Brush, Matthew H and Bug, Bill and Chibucos, Marcus C and Clancy, Kevin and Courtot, M{\'{e}}lanie and Derom, Dirk and Dumontier, Michel and Fan, Liju and Fostel, Jennifer and Fragoso, Gilberto and Gibson, Frank and Gonzalez-Beltran, Alejandra and Haendel, Melissa A and He, Yongqun and Heiskanen, Mervi and Hernandez-Boussard, Tina and Jensen, Mark and Lin, Yu and Lister, Allyson L and Lord, Phillip and Malone, James and Manduchi, Elisabetta and McGee, Monnie and Morrison, Norman and Overton, James A and Parkinson, Helen and Peters, Bjoern and Rocca-Serra, Philippe and Ruttenberg, Alan and Sansone, Susanna-Assunta and Scheuermann, Richard H and Schober, Daniel and Smith, Barry and Soldatova, Larisa N and Stoeckert, Christian J and Taylor, Chris F and Torniai, Carlo and Turner, Jessica A and Vita, Randi and Whetzel, Patricia L and Zheng, Jie},
doi = {10.1371/journal.pone.0154556},
issn = {1932-6203},
journal = {PloS one},
mendeley-groups = {LECA},
number = {4},
pages = {e0154556},
pmid = {27128319},
title = {{The Ontology for Biomedical Investigations.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/27128319 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4851331},
volume = {11},
year = {2016}
}
@techreport{ITIS2015,
author = {ITIS},
pages = {16},
title = {{ITIS Data Model}},
url = {https://www.itis.gov/pdf/ITIS{\_}ConceptualModelEntityDefinition.pdf},
year = {2015}
}
@article{Hinchliff2015,
author = {Hinchliff, Cody E. and Smith, Stephen A. and Allman, James F. and Burleigh, J. Gordon and Chaudhary, Ruchi and Coghill, Lyndon M. and Crandall, Keith A. and Deng, Jiabin and Drew, Bryan T. and Gazis, Romina and Gude, Karl and Hibbett, David S. and Katz, Laura A. and Laughinghouse, H. Dail and McTavish, Emily Jane and Midford, Peter E. and Owen, Christopher L. and Ree, Richard H. and Rees, Jonathan A. and Soltis, Douglas E. and Williams, Tiffani and Cranston, Karen A.},
doi = {10.1073/pnas.1423041112},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
month = {oct},
number = {41},
pages = {12764--12769},
title = {{Synthesis of phylogeny and taxonomy into a comprehensive tree of life}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1423041112},
volume = {112},
year = {2015}
}
@article{Konstantinou2014,
abstract = {Purpose – This paper aims to introduce a transformation engine which can be used to convert an existing institutional repository installation into a Linked Open Data repository. Design/methodology/approach – The authors describe how the data that exist in a DSpace repository can be semantically annotated to serve as a Semantic Web (meta)data repository. Findings – The authors present a non-intrusive, standards-compliant approach that can run alongside with current practices, while incorporating state-of-the art methodologies. Originality/value – Also, they propose a set of mappings between domain vocabularies that can be (re)used towards this goal, thus offering an approach that covers both the technical and semantic aspects of the procedure.},
archivePrefix = {arXiv},
arxivId = {http://dx.doi.org/10.1108/BIJ-10-2012-0068},
author = {Konstantinou, Nikolaos and Spanos, Dimitrios Emmanuel and Houssos, Nikos and Mitrou, Nikolaos},
doi = {10.1108/EL-12-2012-0156},
eprint = {/dx.doi.org/10.1108/BIJ-10-2012-0068},
isbn = {0120130009},
issn = {02640473},
journal = {Electronic Library},
keywords = {DSpace,Linked Open Data,Mapping,Ontology,Relational database,Semantic Web},
number = {6},
pages = {834--851},
pmid = {42012058},
primaryClass = {http:},
title = {{Exposing scholarly information as Linked Open Data: RDFizing DSpace contents}},
volume = {32},
year = {2014}
}
@article{Robertson2014,
author = {Robertson, Tim and D{\"{o}}ring, Markus and Guralnick, Robert and Bloom, David and Wieczorek, John and Braak, Kyle and Otegui, Javier and Russell, Laura and Desmet, Peter},
doi = {10.1371/journal.pone.0102623},
editor = {Little, Damon P.},
issn = {1932-6203},
journal = {PLoS ONE},
mendeley-groups = {LECA},
month = {aug},
number = {8},
pages = {e102623},
title = {{The GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the Internet}},
url = {http://dx.plos.org/10.1371/journal.pone.0102623},
volume = {9},
year = {2014}
}
@article{Konstantinou2013,
abstract = {As far as digital repositories are concerned, numerous benefits emerge from the disposal of their contents as Linked Open Data (LOD). This leads more and more repositories towards this direction. However, several factors need to be taken into account in doing so, among which is whether the transition needs to be materialized in real-time or in asynchronous time intervals. In this paper we provide the problem framework in the context of digital repositories, we discuss the benefits and drawbacks of both approaches and draw our conclusions after evaluating a set of performance measurements. Overall, we argue that in contexts with infrequent data updates, as is the case with digital repositories, persistent RDF views are more efficient than real-time SPARQL-to-SQL rewriting systems in terms of query response times, especially when expensive SQL queries are involved.},
author = {Konstantinou, Nikolaos and Spanos, Dimitrios Emmanuel and Mitrou, Nikolas},
doi = {10.1007/978-3-319-03437-9_33},
isbn = {9783319034362},
issn = {18650929},
journal = {Communications in Computer and Information Science},
keywords = {Bibliographic information,Digital Repositories,Linked Open Data,Mapping,R2RML,RDF Views},
pages = {342--354},
title = {{Transient and Persistent RDF Views over Relational Databases in the Context of Digital Repositories}},
volume = {390 CCIS},
year = {2013}
}
@techreport{TDWG2013,
abstract = {This report constitutes the outcome of the TDWG Vocabulary Management Task Group (VoMaG). It consists of an introduction and four sections. The introduction describes the remit of VoMaG and the three task areas that emerged based on its charter, each of which is dealt with in separate sections. The first area (Section 2) relates to the status of the TDWG Ontology and its relationship to existing TDWG standards. It also examines the Darwin Core Namespace Policy as a means to maintain technical specification standards that define vocabularies, and provides recommendations for actions that would resolve several long-standing issues. The second area (Section 3 and Section 4) deals with the use of Semantic MediaWiki as a community platform for developing and maintaining vocabularies and with the NCBO BioPortal as a tool for sharing ontologies. It looks at the core features provided by MediaWiki, the enhancements provided by the Semantic MediaWiki extension, the implementation of the ViBRANT/GBIF terms wiki on Biowikifarm, and the advantages of BioPortal for ontologies (as opposed to vocabularies). The third area (Section 5) addresses the requirements for a framework for managing vocabularies, identifying the main components and a suggested workflow. Sections include recommendations for consideration by TDWG.},
author = {TDWG},
doi = {10.13140/RG.2.1.1503.7920},
institution = {GBIF},
mendeley-groups = {LECA},
pages = {25},
title = {{Report of the TDWG Vocabulary Management Task Group (VoMaG)}},
url = {www.gbif.org/resource/80862},
year = {2013}
}
@article{Anguita2013,
abstract = {RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.},
author = {Anguita, Alberto and Garc{\'{i}}a-Remesal, Miguel and de la Iglesia, Diana and Maojo, Victor},
doi = {10.1155/2013/983805},
issn = {2314-6133},
journal = {BioMed Research International},
pages = {1--9},
title = {{NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases}},
url = {http://www.hindawi.com/journals/bmri/2013/983805/},
volume = {2013},
year = {2013}
}
@article{Federhen2012,
abstract = {The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.},
author = {Federhen, Scott},
doi = {10.1093/nar/gkr1178},
journal = {Nucleic Acids Research},
keywords = {taxonomic classification},
mendeley-groups = {LECA},
mendeley-tags = {taxonomic classification},
number = {D1},
pages = {136--145},
title = {{The NCBI Taxonomy database}},
url = {https://dx.doi.org/10.1093{\%}2Fnar{\%}2Fgkr1178},
volume = {40},
year = {2012}
}
@article{Sansone2012,
author = {Sansone, Susanna-Assunta and Rocca-Serra, Philippe and Field, Dawn and Maguire, Eamonn and Taylor, Chris and Hofmann, Oliver and Fang, Hong and Neumann, Steffen and Tong, Weida and Amaral-Zettler, Linda and Begley, Kimberly and Booth, Tim and Bougueleret, Lydie and Burns, Gully and Chapman, Brad and Clark, Tim and Coleman, Lee-Ann and Copeland, Jay and Das, Sudeshna and de Daruvar, Antoine and de Matos, Paula and Dix, Ian and Edmunds, Scott and Evelo, Chris T and Forster, Mark J and Gaudet, Pascale and Gilbert, Jack and Goble, Carole and Griffin, Julian L and Jacob, Daniel and Kleinjans, Jos and Harland, Lee and Haug, Kenneth and Hermjakob, Henning and Sui, Shannan J Ho and Laederach, Alain and Liang, Shaoguang and Marshall, Stephen and McGrath, Annette and Merrill, Emily and Reilly, Dorothy and Roux, Magali and Shamu, Caroline E and Shang, Catherine A and Steinbeck, Christoph and Trefethen, Anne and Williams-Jones, Bryn and Wolstencroft, Katherine and Xenarios, Ioannis and Hide, Winston},
doi = {10.1038/ng.1054},
issn = {1061-4036},
journal = {Nature Genetics},
month = {jan},
number = {2},
pages = {121--126},
title = {{Toward interoperable bioscience data}},
url = {http://www.nature.com/doifinder/10.1038/ng.1054},
volume = {44},
year = {2012}
}
@article{Wieczorek2012,
author = {Wieczorek, John and Bloom, David and Guralnick, Robert and Blum, Stan and Döring, Markus and Giovanni, Renato and Robertson, Tim and Vieglais, David},
doi = {10.1371/journal.pone.0029715},
editor = {Sarkar, Indra Neil},
issn = {1932-6203},
journal = {PLoS ONE},
mendeley-groups = {LECA},
month = {jan},
number = {1},
pages = {e29715},
title = {{Darwin Core: An Evolving Community-Developed Biodiversity Data Standard}},
url = {http://dx.plos.org/10.1371/journal.pone.0029715},
volume = {7},
year = {2012}
}
@article{Gaudet2011,
author = {Gaudet, P. and Bairoch, A. and Field, D. and Sansone, S.-A. and Taylor, C. and Attwood, T. K. and Bateman, A. and Blake, J. A. and Bult, C. J. and Cherry, J. M. and Chisholm, R. L. and Cochrane, G. and Cook, C. E. and Eppig, J. T. and Galperin, M. Y. and Gentleman, R. and Goble, C. A. and Gojobori, T. and Hancock, J. M. and Howe, D. G. and Imanishi, T. and Kelso, J. and Landsman, D. and Lewis, S. E. and Mizrachi, I. K. and Orchard, S. and Ouellette, B. F. F. and Ranganathan, S. and Richardson, L. and Rocca-Serra, P. and Schofield, P. N. and Smedley, D. and Southan, C. and Tan, T. W. and Tatusova, T. and Whetzel, P. L. and White, O. and Yamasaki, C.},
doi = {10.1093/nar/gkq1173},
issn = {0305-1048},
journal = {Nucleic Acids Research},
month = {jan},
number = {Database},
pages = {D7--D10},
title = {{Towards BioDBcore: a community-defined information specification for biological databases}},
url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq1173},
volume = {39},
year = {2011}
}
@article{Goff2011,
author = {Goff, Stephen A. and Vaughn, Matthew and McKay, Sheldon and Lyons, Eric and Stapleton, Ann E. and Gessler, Damian and Matasci, Naim and Wang, Liya and Hanlon, Matthew and Lenards, Andrew and Muir, Andy and Merchant, Nirav and Lowry, Sonya and Mock, Stephen and Helmke, Matthew and Kubach, Adam and Narro, Martha and Hopkins, Nicole and Micklos, David and Hilgert, Uwe and Gonzales, Michael and Jordan, Chris and Skidmore, Edwin and Dooley, Rion and Cazes, John and McLay, Robert and Lu, Zhenyuan and Pasternak, Shiran and Koesterke, Lars and Piel, William H. and Grene, Ruth and Noutsos, Christos and Gendler, Karla and Feng, Xin and Tang, Chunlao and Lent, Monica and Kim, Seung-Jin and Kvilekval, Kristian and Manjunath, B. S. and Tannen, Val and Stamatakis, Alexandros and Sanderson, Michael and Welch, Stephen M. and Cranston, Karen A. and Soltis, Pamela and Soltis, Doug and O'Meara, Brian and Ane, Cecile and Brutnell, Tom and Kleibenstein, Daniel J. and White, Jeffery W. and Leebens-Mack, James and Donoghue, Michael J. and Spalding, Edgar P. and Vision, Todd J. and Myers, Christopher R. and Lowenthal, David and Enquist, Brian J. and Boyle, Brad and Akoglu, Ali and Andrews, Greg and Ram, Sudha and Ware, Doreen and Stein, Lincoln and Stanzione, Dan},
doi = {10.3389/fpls.2011.00034},
issn = {1664-462X},
journal = {Frontiers in Plant Science},
title = {{The iPlant Collaborative: Cyberinfrastructure for Plant Biology}},
url = {http://journal.frontiersin.org/article/10.3389/fpls.2011.00034/abstract},
volume = {2},
year = {2011}
}
@article{Constable2010,
author = {Constable, Heather and Guralnick, Robert and Wieczorek, John and Spencer, Carol and Peterson, A. Townsend},
doi = {10.1371/journal.pbio.1000309},
issn = {1545-7885},
journal = {PLoS Biology},
mendeley-groups = {LECA},
month = {feb},
number = {2},
pages = {e1000309},
title = {{VertNet: A New Model for Biodiversity Data Sharing}},
url = {http://dx.plos.org/10.1371/journal.pbio.1000309},
volume = {8},
year = {2010}
}
@unpublished{TDWG2010,
author = {TDWG},
institution = {TDWG},
mendeley-groups = {LECA},
pages = {17},
title = {{TDWG GUID Applicability Statement}},
url = {https://github.com/tdwg/guid-as/blob/master/guid/applicability{\_}statement.doc},
year = {2010}
}
@unpublished{TDWG2009,
author = {TDWG},
institution = {TDWG},
mendeley-groups = {LECA},
pages = {19},
title = {{TDWG Life Sciences Identifiers (LSID) Applicability Statement}},
url = {https://github.com/tdwg/guid-as/blob/master/lsid/applicability{\_}statement.doc},
year = {2009}
}
@article{Page2008,
author = {Page, Roderic DM},
doi = {10.1186/1751-0473-3-2},
issn = {1751-0473},
journal = {Source Code for Biology and Medicine},
number = {1},
pages = {2},
title = {{LSID Tester, a tool for testing Life Science Identifier resolution services}},
url = {http://scfbm.biomedcentral.com/articles/10.1186/1751-0473-3-2},
volume = {3},
year = {2008}
}
@article{Karp2008,
author = {Karp, David R and Carlin, Shelley and Cook-Deegan, Robert and Ford, Daniel E and Geller, Gail and Glass, David N and Greely, Hank and Guthridge, Joel and Kahn, Jeffrey and Kaslow, Richard and Kraft, Cheryl and MacQueen, Kathleen and Malin, Bradley and Scheuerman, Richard H and Sugarman, Jeremy},
doi = {10.1371/journal.pmed.0050190},
issn = {1549-1676},
journal = {PLoS Medicine},
month = {sep},
number = {9},
pages = {e190},
title = {{Ethical and Practical Issues Associated with Aggregating Databases}},
url = {http://dx.plos.org/10.1371/journal.pmed.0050190},
volume = {5},
year = {2008}
}
@article{Ratnasingham2007,
author = {Ratnasingham, Sujeevan and Hebert, Paul D. N.},
doi = {10.1111/j.1471-8286.2007.01678.x},
issn = {14718278},
journal = {Molecular Ecology Notes},
month = {jan},
number = {3},
pages = {355--364},
title = {{BARCODING: bold: The Barcode of Life Data System}},
url = {http://doi.wiley.com/10.1111/j.1471-8286.2007.01678.x},
volume = {7},
year = {2007}
}
@article{Kennedy2006,
author = {Kennedy, J. and Hyam, R. and Kukla, R. and Paterson, T.},
doi = {10.1089/omi.2006.10.220},
issn = {1536-2310},
journal = {OMICS: A Journal of Integrative Biology},
mendeley-groups = {LECA},
month = {jun},
number = {2},
pages = {220--230},
title = {{Standard Data Model Representation for Taxonomic Information}},
url = {http://www.liebertonline.com/doi/abs/10.1089/omi.2006.10.220},
volume = {10},
year = {2006}
}
@article{Page2005,
abstract = {The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.},
author = {Page, Roderic DM},
doi = {10.1186/1471-2105-6-48},
issn = {14712105},
journal = {BMC Bioinformatics},
number = {1},
pages = {48},
title = {{A Taxonomic Search Engine: Federating taxonomic databases using web services}},
url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-6-48},
volume = {6},
year = {2005}
}
@techreport{OMG2004,
author = {OMG},
pages = {32},
title = {{Life Science Identifiers Specifications}},
year = {2004}
}
@techreport{TDWG2004,
author = {{TDWG}},
pages = {14},
title = {{Taxonomic Concept Schema}},
url = {http://tdwg.napier.ac.uk/doc/tdwg{\_}tcs.pdf},
year = {2004}
}
@techreport{NIH2002,
author = {{National Human Genome Research Institute}},
mendeley-groups = {LECA},
title = {{Report from the NIH/NIAID/Wellcome Trust Workshop on Model Organism Databases}},
url = {https://www.genome.gov/10006356/mod-workshop-report/},
year = {2002}
}
@incollection{Jones2000,
address = {Berlin, Heidelberg},
author = {Jones, Andrew C and Xu, Xuebiao and Pittas, Nick and Gray, W Alex and Fiddian, Nick J and White, Richard J and Robinson, John and Bisby, Frank A and Brandt, Sue M},
booktitle = {Database and Expert Systems Applications: 11th International Conference, DEXA 2000 London, UK, September 4--8, 2000 Proceedings},
doi = {10.1007/3-540-44469-6_92},
editor = {Ibrahim, Mohamed and K{\"{u}}ng, Josef and Revell, Norman},
isbn = {978-3-540-44469-5},
pages = {981--992},
publisher = {Springer Berlin Heidelberg},
title = {{SPICE: A Flexible Architecture for Integrating Autonomous Databases to Comprise a Distributed Catalogue of Life}},
url = {http://dx.doi.org/10.1007/3-540-44469-6{\_}92},
year = {2000}
}