Access to biological collection data ABCD Schema 2.06 ? ratified TDWG Standard, Botanischer Garten und Botanisches Museum Berlin- Dahlem (BGBM), 2007. ,
Annotating biodiversity data via the Internet, Taxon, vol.62, issue.6, pp.1248-1258, 2013. ,
DOI : 10.12705/626.4
AnnoSys implementation of a generic annotation system for schema-based data using the example of biodiversity collection data, Database, pp.10-1093, 2017. ,
The Description Logic Handbook: Theory, Implementation, and Applications, 2003. ,
DOI : 10.1017/CBO9780511711787
Darwin-SW: Darwin Core-based terms for expressing biodiversity data as RDF, Semantic Web, vol.11, issue.1, pp.617-627, 2016. ,
DOI : 10.1371/journal.pone.0029715
The Emerging Web of Linked Data, IEEE Intelligent Systems, vol.24, issue.5, pp.87-92, 2009. ,
DOI : 10.1109/MIS.2009.102
The Encyclopedia of Life: Describing Species, Unifying Biology, BioScience, vol.59, issue.7, pp.551-556, 2009. ,
DOI : 10.1525/bio.2009.59.7.4
Presenting and preserving the change in taxonomic knowledge for linked data, Semantic Web, vol.73, issue.1, pp.589-616, 2016. ,
DOI : 10.1111/j.1095-8312.2001.tb01348.x
The NCBI Taxonomy database, Nucleic Acids Research, vol.270, issue.1512, pp.136-143, 2012. ,
DOI : 10.1098/rspb.2002.2218
URL : https://academic.oup.com/nar/article-pdf/40/D1/D136/9480848/gkr1178.pdf
TAXREF v10. 0, référentiel taxonomique pour la France: méthodologie, mise en oeuvre et diffusion, Muséum National d'Histoire Naturelle, 2016. ,
Bizer: Linked Data: Evolving the Web into a Global Data Space, 2011. ,
DOI : 10.2200/s00334ed1v01y201102wbe001
Reusing the NCBO BioPortal technology for agronomy to build AgroPortal, Proceedings of the 7th International Conference on Biomedical Ontologies, ICBO'16, Demo Session, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01398251
Seeliger: International Code of Nomenclature of Bacteria: Bacteriological Code -1990 Revision, 1992. ,
DBpedia -A Large-scale, Multilingual Knowledge Base Extracted from Wikipedia, Semantic Web, pp.167-195, 2014. ,
International Code of Nomenclature for algae, fungi, and plants (Melbourne Code), Regnum Vegetabile, vol.154, 2012. ,
Montagnat: Translation of Heterogeneous Databases into RDF, and Application to the Construction of a SKOS Taxonomical Reference, Revised Selected Papers of the 11th International Conference on Web Information Systems and Technologies (WebIST), pp.275-296, 2016. ,
The Vertebrate Taxonomy Ontology: a framework for reasoning across model organism and species phenotypes, Journal of Biomedical Semantics, vol.4, issue.34, 2013. ,
Kobilarov: Silk -A Link Discovery Framework for the Web of Data, 2nd Workshop about Linked Data on the Web, 2009. ,
Darwin Core: An Evolving Community-Developed Biodiversity Data Standard, PLoS ONE, vol.247, issue.5, 2012. ,
DOI : 10.1371/journal.pone.0029715.g002
URL : https://doi.org/10.1371/journal.pone.0029715
Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens, Database, vol.3, pp.1-19, 2015. ,
DOI : 10.11646/phytotaxa.73.1.4
Devising the EDIT Platform for Cybertaxonomy Tools for Identifying Biodiversity: Progress and Problems, roceedings of the International Congress, pp.20-22, 2010. ,
Impact of a Century of Climate Change on Small-Mammal Communities in Yosemite National Park, USA, Science, vol.84, issue.2, 2008. ,
DOI : 10.1086/518948
The tropicalization of temperate marine ecosystems: climate-mediated changes in herbivory and community phase shifts, Proc. R. Soc. B, 2014. ,
DOI : 10.1111/j.1466-822X.2006.00212.x
Rationale and Value of Natural History Collections Digitisation, Biodiversity Informatics, vol.7, issue.2, 2010. ,
DOI : 10.17161/bi.v7i2.3994
URL : https://journals.ku.edu/jbi/article/download/3994/3811
Darwin Core: An Evolving Community-Developed Biodiversity Data Standard, PLoS ONE, vol.247, issue.5, 2012. ,
DOI : 10.1371/journal.pone.0029715.g002
URL : https://doi.org/10.1371/journal.pone.0029715
The GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the Internet, PLoS ONE, vol.25, issue.11, 2014. ,
DOI : 10.1371/journal.pone.0102623.g004
The Semantic Web, Scientific American, vol.284, issue.5, 2001. ,
DOI : 10.1038/scientificamerican0501-34
Linked data-the story so far. Semantic services, interoperability and web applications: emerging concepts, 2009. ,
DOI : 10.4018/jswis.2009081901
URL : https://eprints.soton.ac.uk/271285/1/bizer-heath-berners-lee-ijswis-linked-data.pdf
Bio2RDF: Towards a mashup to build bioinformatics knowledge systems, Journal of Biomedical Informatics, vol.41, issue.5, 2008. ,
DOI : 10.1016/j.jbi.2008.03.004
URL : https://doi.org/10.1016/j.jbi.2008.03.004
Biological Names and Taxonomies on the Semantic Web ??? Managing the Change in Scientific Conception??, 2011. ,
DOI : 10.1007/978-3-642-02121-3_57
Darwin Core Archive How-To Guide, 2011. ,
Using OpenRefine, 2013. ,
OWLIM: A family of scalable semantic repositories, Semantic Web, 2011. ,
Managing the Life-Cycle of Linked Data with the LOD2 Stack, International Semantic Web Conference Lecture Notes in Computer Science, 2012. ,
DOI : 10.1007/978-3-642-35173-0_1
Dublin core metadata element set, version 1.1, 2012. ,
Best practice for biodiversity data management and publication, Biological Conservation, 2014. ,
Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science, ZooKeys, 2012. ,
Natural History Specimen Digitization: Challenges and Concerns, Biodiversity Informatics, vol.7, issue.2, 2010. ,
DOI : 10.17161/bi.v7i2.3992
URL : https://journals.ku.edu/jbi/article/download/3992/3806
DBpedia: A Nucleus for a Web of Open Data. The Semantic Web, 2007. ,
W3C Semantic Web Interest Group: Basic Geo (WGS84 lat/long) Vocabulary, 2011. ,
Geonames ontology, 2015. ,
The Friend Of A Friend (FOAF) vocabulary specification, 2007. ,
Darwin-SW: Darwin Core-based terms for expressing biodiversity data as RDF. Semantic Web, 2016. ,
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation, Journal of Biomedical Semantics, vol.3, issue.2, 2016. ,
DOI : 10.1038/sdata.2016.18
The NCBI Taxonomy database, Nucleic Acids Research, vol.270, issue.1512, 2012. ,
DOI : 10.1098/rspb.2002.2218
URL : https://academic.oup.com/nar/article-pdf/40/D1/D136/9480848/gkr1178.pdf
What are semantic annotations, 2006. ,
Where to publish and find ontologies? A survey of ontology libraries, Web Semantics: Science, Services and Agents on the World Wide Web, pp.96-111, 2012. ,
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications, Nucleic Acids Research, vol.140, issue.1, 2011. ,
DOI : 10.1104/pp.105.063008
A new Ontology Lookup Service at EMBL-EBI, Proceedings of SWAT4LS International Conference 2015, pp.118-119, 2015. ,
EnvThes-interlinked thesaurus for long term ecological research, monitoring, and experiments, Proceedings of the 27th Int'l Conference on Environmental Informatics, Shaker, 2013. ,
Fostering ecological data sharing: collaborations in the International Long Term Ecological Research Network, Ecosphere, vol.6, issue.10, pp.1-18, 2015. ,
DOI : 10.1146/annurev.ecolsys.34.012103.144032
EcoSemanticPortal: facilitating discovery and interoperability of ontologies and thesauri in the ecological domain, Proc. of the 2nd International Workshop on Semantics for Biodiversity ,
Reusing the NCBO BioPortal technology for agronomy to build AgroPortal, Proceedings of the 7th International Conference on Biomedical Ontologies (ICBO-BioCreative), CEUR-WS, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01398251
Publishing SKOS vocabularies with Skosmos Article manuscript submitted for review, http://skosmos.org/publishing-skosvocabularies-with-skosmos .pdf, last accessed, 2017. ,
Linked Open Vocabularies (LOV): A gateway to reusable semantic vocabularies on the Web, Semantic Web, vol.39, issue.Suppl, pp.437-452, 2017. ,
DOI : 10.1093/nar/gkr469
SISSVoc: A Linked Data API for access to??SKOS vocabularies, Semantic Web, vol.4, issue.1, pp.9-24, 2016. ,
DOI : 10.1007/s12145-011-0084-5
URL : http://semantic-web-journal.net/system/files/swj819.pdf
Ontobee: A Linked Data Server and Browser for Ontology Terms, Proceedings of the 2nd International Conference on Biomedical Ontologies (ICBO), CEUR-WS, pp.279-281, 2011. ,
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology, vol.10, issue.11, pp.1251-1255, 2007. ,
DOI : 10.1093/bioinformatics/btm155
Ontology Metadata Vocabulary and Applications, On the Move to Meaningful Internet Systems 2005: OTM 2005 Workshops. OTM 2005, pp.906-915, 2005. ,
DOI : 10.1007/11575863_112
URL : http://oyster.ontoware.org/oyster/omv-otm.pdf
Hydra: A Vocabulary for Hypermedia-Driven Web APIs, Proceedings of the WWW2013 Workshop on Linked Data on the Web, CEUR-WS, 2013. ,
DOI : 10.1007/978-1-4614-9299-3_7
A Web API ecosystem through feature-based reuse. arXiv preprint, p.arXiv, 2016. ,
Swoogle: Searching for knowledge on the semantic web, Proceedings of the 20th National Conference on Artificial Intelligence, pp.1682-1683, 2005. ,
Falcons, Proceeding of the 17th international conference on World Wide Web , WWW '08, pp.1101-1102, 2008. ,
DOI : 10.1145/1367497.1367676
Watson: Supporting next generation semantic web applications, Proceedings of the IADIS International Conference on WWW/Internet, 2007. ,
A Network of Ontology Repositories, 2010. ,
OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript, BMC Bioinformatics, vol.12, issue.1, p.218, 2011. ,
DOI : 10.1186/1471-2105-8-S9-S5
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-218?site=bmcbioinformatics.biomedcentral.com
Ontohub -a repository engine for heterogeneous ontologies and alignments ,
A systematic analysis of term reuse and term overlap across biomedical ontologies, Semantic Web, 2017. ,
DOI : 10.1186/1756-0500-3-175
Identifiers for the 21st century: How to design , provision, and reuse persistent identifiers to maximize utility and impact of life science data, PLoS Biology, issue.6, p.15, 2017. ,
Creating Mappings for Ontologies in Biomedi-cine: Simple Methods Work, AMIA Annual Symposium Proceedings, pp.198-202, 2009. ,
Improving biodiversity data retrieval through semantic search and ontologies, ACM International Joint Conferences on Web Intelligence (WI) and Intelligent Agent Technologies (IAT), pp.274-281, 2014. ,
Hybrid Search: Effectively Combining Keywords and Semantic Searches, 5th European Semantic Web Conference, ESWC, pp.554-568, 2008. ,
DOI : 10.1007/978-3-540-68234-9_41
URL : http://eprints.whiterose.ac.uk/3771/1/ESWC08.pdf
Integrating Keywords and Semantics on Document Annotation and Search, On the Move to Meaningful Internet Systems, OTM 2010 -Confederated International Conferences Proceedings , Part II, pp.921-938, 2010. ,
DOI : 10.1007/978-3-642-13489-0_27
URL : http://web.imis.athena-innovation.gr/%7Edalamag/pub/bgds-odbase10.pdf
A fast rule-based approach for biomedical event extraction, Proceedings of the BioNLP, 2013. ,
An Adaptation of the Vector-Space Model for Ontology-Based Information Retrieval, IEEE Transactions on Knowledge and Data Engineering, vol.19, issue.2, pp.261-272, 2007. ,
DOI : 10.1109/TKDE.2007.22
A conceptual model for data management in the field of ecology, Ecological Informatics, vol.24, pp.261-272, 2014. ,
DOI : 10.1016/j.ecoinf.2013.12.003
Selecting and Tailoring Ontologies with JOYCE, Proc. of the Intl. Conf. on Knowledge Engineering and Knowledge Management, 2017. ,
DOI : 10.1145/1242572.1242669
<italic>TextTile</italic>: An Interactive Visualization Tool for Seamless Exploratory Analysis of Structured Data and Unstructured Text, IEEE Transactions on Visualization and Computer Graphics, vol.23, issue.1, pp.161-170, 2017. ,
DOI : 10.1109/TVCG.2016.2598447
Bridging structured and unstructured data via hybrid semantic search and interactive ontology-enhanced query formulation, Knowledge and Information Systems, vol.7, issue.3, pp.761-792, 2014. ,
DOI : 10.1016/j.websem.2009.07.005
LINNAEUS: A species name identification system for biomedical literature, BMC Bioinformatics, vol.11, issue.1, p.85, 2010. ,
DOI : 10.1186/1471-2105-11-85
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-85?site=bmcbioinformatics.biomedcentral.com
Semantic search, Proceedings of the twelfth international conference on World Wide Web , WWW '03, pp.700-709, 2003. ,
DOI : 10.1145/775152.775250
Grounding Epistemic Modality in Speakers??? Judgments, Trends in Artificial Intelligence. PRICAI 2014 ?Proceedings of the 13th Pacific Rim International Conference on Artificial Intelligence. Gold Coast number 8862 in Lecture Notes in Artificial Intelligence, pp.654-667, 2014. ,
DOI : 10.1007/978-3-319-13560-1_52
UIMA-based JCoRe 2.0 goes GitHub and Maven Central: State-of-the-art software resource engineering and distribution of NLP pipelines, Proc. of the Intl. Conf. on Language Resources and Evaluation, pp.2502-2509, 2016. ,
The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011, BMC Bioinformatics, vol.13, issue.Suppl 11, p.1, 2012. ,
DOI : 10.1186/1471-2105-13-S11-S1
How Deep Can Surface Signals Be Traced in the Critical Zone? Merging Biodiversity with Biogeochemistry Research in a Central German Muschelkalk Landscape, Frontiers in Earth Science, vol.304, p.32, 2016. ,
DOI : 10.1126/science.1097394
An ontology for describing and synthesizing ecological observation data, Ecological Informatics, vol.2, issue.3, pp.279-296, 2007. ,
DOI : 10.1016/j.ecoinf.2007.05.004
URL : http://obs.ecoinformatics.org/attach?page=Projects%2Foboe_ecological_informatics.pdf
Answering top-K query combined keywords and structural queries on RDF graphs, Information Systems, vol.67, pp.19-35, 2017. ,
DOI : 10.1016/j.is.2017.03.002
On the Marriage of SPARQL and Keywords, Web Technologies and Applications -17th Asia-PacificWeb Conference Proceedings, pp.3-16, 2015. ,
DOI : 10.1145/2588555.2610525
Semantic Web in data mining and knowledge discovery: A comprehensive survey, Journal of Web Semantics: Science, Services and Agents on the World Wide Web, pp.1-22, 2016. ,
DOI : 10.1016/j.websem.2016.01.001
A SIMPLE ALGORITHM FOR IDENTIFYING ABBREVIATION DEFINITIONS IN BIOMEDICAL TEXT, Biocomputing 2003, pp.451-462, 2003. ,
DOI : 10.1142/9789812776303_0042
Semantic Bridges for Biodiversity Sciences, The Semantic Web -ISWC 2015 -14th International Semantic Web Conference Proceedings, Part II, pp.310-317, 2015. ,
DOI : 10.1371/journal.pone.0089606
High-performance gene name normalization with GENO, Bioinformatics, vol.23, issue.8, pp.815-821, 2009. ,
DOI : 10.1093/bioinformatics/btm056
URL : https://academic.oup.com/bioinformatics/article-pdf/25/6/815/701154/btp071.pdf
The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries, BMC Bioinformatics, vol.7, issue.1, pp.1-7, 2006. ,
Towards an integrated biodiversity and ecological research data management and archiving platform: The german federation for the curation of biological data (gfbio) ,
Aber-OWL: a framework for ontology-based data access in biology, BMC Bioinformatics, vol.25, issue.1-2, pp.1-9, 2015. ,
DOI : 10.1007/s00335-013-9481-z
Reusing the NCBO BioPortal technology for agronomy to build AgroPortal, ICBO : International Conference on Biomedical Ontologies, p.3, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01398251
A Terminology Service Supporting Semantic Annotation, Integration, Discovery and Analysis of Interdisciplinary Research Data, Datenbank-Spektrum, vol.2, issue.3, pp.195-205, 2016. ,
DOI : 10.1016/j.ecoinf.2007.07.005
Honey Bee Versus Apis Mellifera: A Semantic Search for Biological Data ,
DOI : 10.1007/s13222-016-0231-8
BioPortal: ontologies and integrated data resources at the click of a mouse, Nucleic Acids Research, vol.36, issue.suppl_2, pp.170-173, 2009. ,
DOI : 10.1093/nar/gkn317
URL : https://hal.archives-ouvertes.fr/hal-00492020
Deploying national ontology services: From onki to finto, Proceedings of the Industry Track at the International Semantic Web Conference 2014. CEUR Workshop Proceedings, 2014. ,
Towards an integrated biodiversity and ecological research data management and archiving platform: GFBio, 2014. ,
An ontology for describing and synthesizing ecological observation data, Ecological Informatics, vol.2, issue.3, 2007. ,
DOI : 10.1016/j.ecoinf.2007.05.004
URL : http://obs.ecoinformatics.org/attach?page=Projects%2Foboe_ecological_informatics.pdf
Introduction to Information Retrieval, 2008. ,
DOI : 10.1017/CBO9780511809071
Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies, PLoS ONE, vol.23, issue.1, p.89606, 2014. ,
DOI : 10.1371/journal.pone.0089606.s001
The FAIR Guiding Principles for scientific data management and stewardship, Scientific Data, vol.22, issue.2012, p.2016, 160018. ,
DOI : 10.7717/peerj-cs.1
URL : http://www.nature.com/articles/sdata201618.pdf
Small Big Data: Using multiple data-sets to explore unfolding social and economic change. Big Data & Society, 2015. ,
DOI : 10.1177/2053951715589418
URL : https://doi.org/10.1177/2053951715589418
When more is better: how data sharing would accelerate genomic selection of crop plants, New Phytologist, vol.124, issue.4, 2016. ,
DOI : 10.1007/s00122-011-1745-y
Available: http://www.bioversityinternational.org/e-library/publications/detail/faobioversity-multi- crop-passport-descriptors-v21-mcpd-v21, pp.8-2017, 2012. ,
Registries of domain-relevant semantic reference models help bootstrap interoperability in domains with fragmented data resources, Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016. ,
Trends in ex situ conservation of plant genetic resources: a review of global crop and regional conservation strategies, Genetic Resources and Crop Evolution, vol.85, issue.2, pp.625-639, 2010. ,
DOI : 10.1007/BF00223704
Surfing the Genepool: the Effective and Efficient Use of Plant Genetic Resources, 2011. ,
Ontology for observations and sampling features, with alignments to existing models, Semantic Web, pp.453-470, 2017. ,
DOI : 10.5194/adgeo-8-83-2006
Introducing the Next Generation of Ecosystem Research in Europe: LTER- Europe's Multi-Functional and Multi-Scale Approach (eds) Long-Term Ecological Research, pp.10-1007, 2010. ,
Monitoring of Environmental Status through Long Term Series: Data Management System in the EnvEurope Project, Proceedings EnviroInfo 2012, pp.293-301, 2012. ,
SERONTO: A Socio-Ecological Research and observation oNTOlogy, Proceedings of TDWG. Fremantle, Australia, 2008. ,
EnvThes -interlinked thesaurus for long term ecological research, monitoring, and experiments, Proceedings EnviroInfo 2013: Environmental Informatics and Renewable Energies, pp.824-832, 2013. ,
Where to Publish and Find Ontologies? A Survey of Ontology Libraries, In Web Semant, vol.11, pp.96-111, 2012. ,
Goal-driven requirements analysis for hypermedia-intensive Web applications, Requirements Engineering, vol.9, issue.2, pp.85-103, 2004. ,
DOI : 10.1007/s00766-004-0188-2
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology, issue.11, pp.25-1251, 2007. ,