doi:10.1017/S0269888920000132

Alves , C., Castro , J. A., Ribeiro , C., Honrado , J. P. & Lomba , A.2018. Research data management in the field of ecology: an overview. In Proceedings of the International Conference on Dublin Core and Metadata Applications.

Annane , A., Bellahsene , Z., Azouaou , F. & Jonquet , C.2016. Selection and combination of heterogeneous mappings to enhance biomedical ontology matching. In Knowledge Engineering and Knowledge Management - 20th International Conference, EKAW ’16, Bologna, Italy, November19–23, 2016, Proceedings.

Arnaud. , E., Cooper. , L., Shrestha. , R., Menda. , N., Nelson. , R. T., Matteis. , L., Skofic. , M., Bastow. , R., Jaiswal. , P., Mueller. , L. & McLaren. , G.2012. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes. In Proceedings of the International Conference on Knowledge Engineering and Ontology Development - Volume 1: KEOD, (IC3K ’12). INSTICC, SciTePress.

Arnold , P. & Rahm , E.2014. Enriching ontology mappings with semantic relations. Data & Knowledge Engineering93, 1–18. Selected Papers from the 17th East--European Conference on Advances in Databases and Information Systems.

Bodenreider , O.2004. The unified medical language system (UMLS): integrating biomedical terminology, Nucleic AcidsResearch32(Database-Issue), 267–270.

Bruelheide , H., Dengler , J., Purschke , O., Lenoir , J., Jiménez-Alfaro , B, Hennekens , S. M., Botta-Dukét , Z., Chytrý , M., Field , R., Jansen , F., Kattge , J., Pillar , V. D., Schrodt , F., Mahecha , M. D., Peet , R. K., Sandel , B., van Bodegom , P., Altman , J., Alvarez-Dávila , E., Arfin Khan , M. A. S., Attorre , F., Aubin , I., Baraloto , C., Barroso , J. G., Bauters , M., Bergmeier , E., Biurrun , I., Bjorkman , A. D., Blonder , B., Čarni , A., Cayuela , L., Černý , T., Cornelissen , J. H. C., Craven , D., Dainese , M., Derroire , G., De Sanctis , M., Díaz , S., Doležal , J., Farfan-Rios , W., Feldpausch , T. R., Fenton , N. J., Garnier , E., Guerin , G. R., Gutiérrez , A. G., Haider , S., Hattab , T., Henry , G., Hérault , B., Higuchi , P., Hölzel , N., Homeier , J., Jentsch , A., Jürgens , N., Kącki , Z., Karger , D. N., Kessler , M., Kleyer , M., Knollová , I., Korolyuk , A. Y., Kühn , I., Laughlin , D. C., Lens , F., Loos , J., Louault , F., Lyubenova , M. I., Malhi , Y., Marcenò , C., Mencuccini , M., Müller , J. V., Munzinger , J., Myers-Smith , I. H.,Neill , D. A., Niinemets , Ü., Orwin , K. H., Ozinga , W. A., Penuelas , J., Pérez-Haase , A., Petřík , P., Phillips , O. L., Pärtel , M., Reich , P B., Römermann , C., Rodrigues , A. V., Sabatini , F. M., Sardans , J., Schmidt , M., Seidler , G., Silva Espejo , J. E., Silveira , M., Smyth , A., Sporbert , M., Svenning , J., Tang , Z., Thomas , R., Tsiripidis , I., Vassilev , K., Violle , C., Virtanen , R., Weiher , E., Welk , E., Wesche , K., Winter , M., Wirth , C. & Jandt , U.2018. Global trait-environment relationships of plant communities. Nature Ecology & Evolution2, 1906–1907.

Buttigieg , P. L., Morrison , N., Smith , B., Mungall , C. J. & Lewis , S. E.2013a. The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics4(1), 43:1–43:9.

Buttigieg , P. L., Pafilis , E., Lewis , S. E., Schildhauer , M. P., Walls , R. L. & Mungall , C. J.2013b. The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. Journal of Biomedical Semantics7(1), 57:1–57:12.

Cooper , L., Meier , A., Laporte , M.-A., Elser , J. L., Mungall , C., Sinn , B. T., Cavaliere , D., Carbon , S., Dunn , N. A., Smith , B., Qu , B., Preece , J., Zhang , E., Todorovic , S., Gkoutos , G., Doonan , J. H., Stevenson , D. W., Arnaud , E. & Jaiswal , P.2018. The planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Research46(D1), D1168–D1180.

Cooper , L., Walls , R. L., Elser , J., Gandolfo , M. A., Stevenson , D. W., Smith , B., Preece , J., Athreya , B., Mungall , C. J., Rensing , S., Hiss , M., Lang , D., Reski , R., Berardini , T. Z., Li , D., Huala , E., Schaeffer , M., Menda , N., Arnaud , E., Shrestha , R., Yamazaki , Y. & Jaiswal , P.2013. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant and Cell Physiology54(2), e1.

Dahdul , W. M., Manda , P., Cui , H., Balhoff , J. P., Dececchi , T. A., Ibrahim , N., Lapp , H., Vision , T. J. & Mabee , P. M.2018. Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. Database 2018.

David , J., Euzenat , J., Scharffe , F. & dos Santos , C. T. 2011. The alignment API 4.0. Semantic Web 2(1), 3–10.

Diaz , S., Purvis , A., Cornelissen , J. H. C., Mace , G. M., Donoghue , M. J., Ewers , R. M., Jordano , P. & Pearse , W. D.2013. Functional traits, the phylogeny of function, and ecosystem service vulnerability. Ecology and Evolution 3(9), 2958–2975.

Diepenbroek , M., Glöckner , F. O., Grobe , P., Güntsch , A., Huber , R., König-Ries , B., Kostadinov , I., Nieschulze , J., Seeger , B., Tolksdorf , R. & Triebel , D.2014. Towards an integrated biodiversity and ecological research data management and archiving platform: the German Federation for the Curation of Biological Data (GFBio). In 44. Jahrestagung der Gesellschaft für Informatik, Informatik 2014, Big Data - KomplexitÄt meistern, September 22–26, 2014, Stuttgart, Deutschland, pp. 1711–1721.

Diepenbroek , M., Schindler , U., Huber , R., Pesant , S., Stocker , M., Felden , J., Buss , M. & Weinrebe , M.2017. Terminology supported archiving and publication of environmental science data in PANGAEA.Journal of Biotechnology261, 177–186.

DiGiuseppe , N., Pouchard , L. C. & Noy , N. F.2014. SWEET ontology coverage for earth system sciences. Earth Science Informatics7(4), 249–264.

Djeddi , W. E. & Khadir , M. T.2014. A novel approach using context-based measure for matching large scale ontologies. In Data Warehousing and Knowledge Discovery - 16th International Conference, DaWaK 2014, Munich, Germany, September 2–4, 2014. Proceedings.

Djeddi , W. E., Khadir , M. T. & Yahia , S. B.2018. XMap results for OAEI 2018. In Proceedings of the 13th International Workshop on Ontology Matching Co-located with the 17th International Semantic Web Conference (ISWC ’18), USA, 2018.

Dragisic , Z., Ivanova , V., Lambrix , P., Faria , D., Jiménez-Ruiz , E. & Pesquita , C.2016. User validation in ontology alignment. In International Semantic Web Conference.

Duchateau , F. & Bellahsene , Z.2016. YAM: a step forward for generating a dedicated schema matcher. Trans. Large-Scale Data- and Knowledge-Centered Systems25. 10.1007/978-3-662-49534-6_5.

Ehrig , M.2006. Ontology alignment: bridging the semantic gap. In Semantic Web and Beyond: Computing for Human Experience. 10.1007/978-0-387-36501-5

Ehrig , M.2007. Ontology Alignment: Bridging the Semantic Gap, Semantic Web and Beyond: Computing for Human Experience 4, Springer.

Euzenat , J. & Shvaiko , P.2013. Ontology Matching, 2nd Edition. Springer.

Faria , D., Pesquita , C., Santos , E., Cruz , I. F. & Couto , F. M.2014. AgreementMakerLight 2.0: towards efficient large-scale ontology matching. In Proceedings of the ISWC 2014 Posters & Demonstrations Track a track within the 13th International Semantic Web Conference, ISWC ’14.

Faria , D., Pesquita , C., Santos , E., Palmonari , M., Cruz , I. F. & Couto , F. M.2013. The AgreementMakerLight ontology matching system. In On the Move to Meaningful Internet Systems: OTM 2013 Conferences - Confederated International Conferences: CoopIS, DOA-Trusted Cloud, and ODBASE.

Fichtmüller , D., Gleisberg , M., Karam , N., Müller-Birn , C. & Güntsch , A.2017. Terminologies as a neglected part of research data: making supplementary research data available through the GFBio terminology service. In Proceedings of the 2nd International Workshop on Semantics for Biodiversity Co-located with 16th International Semantic Web Conference (ISWC ’17), Vienna, Austria, October 22, 2017.

Ghazvinian , A., Noy , N. F. & Musen , M. A.2009. Creating mappings for ontologies in biomedicine: Simple methods work. In AMIA ’09, American Medical Informatics Association Annual Symposium, San Francisco, CA, USA, November 14–18, 2009. AMIA.

Gkoutos , G. V., Green , E. C. J., Mallon , A.-M., Hancock , J. M. & Davidson , D.2005. Using ontologies to describe mouse phenotypes. Genome Biol6(1), R8–R8. https://www.ncbi.nlm.nih.gov/pubmed/15642100.

Grau , B. C., Horrocks , I., Motik , B., Parsia , B., Patel-Schneider , P. F. & Sattler , U.2008. OWL 2: the next step for OWL. Journal of Web Semantics6(4), 309–322.

Harrow , I., Jiménez-Ruiz , E., Splendiani , A., Romacker , M., Woollard , P., Markel , S., Alam-Faruque , Y., Koch , M., Malone , J. & Waaler , A.2017. Matching disease and phenotype ontologies in the ontology alignment evaluation initiative. Journal of Biomedical Semantics8(1), 55:1–55:13.

Hickey , L. J.1973. Classification of the architecture of dicotyledonous leaves. American Journal of Botany60(1), 17–33.

Hoehndorf , R., Alshahrani , M., Gkoutos , G. V., Gosline , G., Groom , Q., Hamann , T., Kattge , J., de Oliveira , S. M., Schmidt , M., Sierra , S., Smets , E., Vos , R. A. & Weiland , C.2016. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. Journal of Biomedical Semantics7(1), 65.

Hoehndorf , R., Weiland , C., Schmidt , M., Groom , Q., Gosline , G., Dressler , S. & Hamann , T.2018. The Flora Phenotype Ontology (FLOPO) and the FLOPO knowledgebase. In Application of Semantic Technology in Biodiversity Science, Thessen , A. E. (ed). IOS Press, Chapter 6, pp. 107–119.

IPBES2018. The IPBES assessment report on land degradation and restoration.

Jiménez-Ruiz , E. & Grau , B. C.2011. LogMap: logic-based and scalable ontology matching. In 10th International Semantic Web Conference, ISWC ’11, pp. 273–288.

Jiménez-Ruiz , E., Grau , B. C. & Horrocks , I.2013. Is my ontology matching system similar to yours? In Proceedings of the 8th International Workshop on Ontology Matching Co-located with the 12th International Semantic Web Conference (ISWC 2013), Sydney, Australia, October 21, 2013, Shvaiko, P., Euzenat, J., Srinivas, K., Mao, M. & Jiménez-Ruiz, E. (eds), CEUR Workshop Proceedings 1111. CEUR-WS.org, pp. 229–230.

Kalfoglou , Y. & Schorlemmer , W. M.2005. Ontology mapping: the state of the art. In Semantic Interoperability and Integration.

Karam , N., Müller-Birn , C., Gleisberg , M., Fichtmüller , D., Tolksdorf , R. & Güntsch , A.2016. A terminology service supporting semantic annotation, integration, discovery and analysis of interdisciplinary research data. Datenbank-Spektrum16(3), 195–205.

Kattge , J., Ogle , K., Bnisch , G., Daz , S., Lavorel , S., Madin , J., Nadrowski , K., Nllert , S., Sartor , K. & Wirth , C.2011. A generic structure for plant trait databases. Methods in Ecology and Evolution2(2), 202–213.

Kibbe , W. A., Arze , C., Felix , V., Mitraka , E., Bolton , E., Fu , G., Mungall , C. J., Binder , J. X., Malone , J., Vasant , D., Parkinson , H. E. & Schriml , L. M.2015. Disease ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Research43(Database-Issue), 1071–1078.

Klan , F., Faessler , E., Algergawy , A., König-Ries , B. & Hahn , U.2017. Integrated semantic search on structured and unstructured data in the adonis system. In Proceedings of the 2nd International Workshop on Semantics for Biodiversity Co-located with 16th International Semantic Web Conference (ISWC ’17), Vienna, Austria, October 22, 2017.

Laadhar , A., Ghozzi , F., Megdiche , I., Ravat , F., Teste , O. & Gargouri , F.2017. Pomap: An effective pairwise ontology matching system. In Proceedings of the 9th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management - (Volume 2), Funchal, Madeira, Portugal, November 1–3, 2017.

Löffler , F., Pfaff , C., Karam , N., Fichtmüller , D. & Klan , F.2017. What do biodiversity scholars search for? Identifying high-level entities for biological metadata. In Proceedings of the 2nd International Workshop on Semantics for Biodiversity Co-located with 16th International Semantic Web Conference (ISWC ’17), Vienna, Austria, October 22, 2017.

Meilicke , C.2011. Alignment Incoherence in Ontology Matching. PhD thesis, University of Mannheim.

Melnik , S., Garcia-Molina , H. & Rahm , E.2002. Similarity flooding: a versatile graph matching algorithm and its application to schema matching. In ICDE ’02.

Mikolov , T., Sutskever , I., Chen , K., Corrado , G. & Dean , J.2013. Distributed representations of words and phrases and their compositionality. In Proceedings of the 26th International Conference on Neural Information Processing Systems -Volume 2, NIPS ’13. Curran Associates Inc., USA.

Mungall , C. J., Torniai , C., Gkoutos , G. V., Lewis , S. E. & Haendel , M. A.2012. Uberon, an integrative multi-species anatomy ontology. Genome Biology13(1), R5.

Musen , M. A.2015. The Protégé project: a look back and a look forward. AI Matters1(4), 4–12.

Raskin , R. G. & Pan , M. J.2004. Knowledge representation in the semantic web for earth and environmental terminology (SWEET).Computers & Geosciences31(9), 1119–1125.

Shvaiko , P. & Euzenat , J.2013. Ontology matching: State of the art and future challenges. IEEE Transactions on Knowledge and Data Engineering25(1), 158–176.

Smaili , F. Z., Gao , X. & Hoehndorf , R.2018. OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. CoRRabs/1804.10922.

Solimando , A., Jiménez-Ruiz , E. & Guerrini , G.2017. Minimizing conservativity violations in ontology alignments: algorithms and evaluation. Knowledge and Information Systems51(3), 775–819.

Stevens , P. F. Glossary of the angiosperm phylogeny website, New York Botanical Garden. https://sweetgum.nybg.org/science/glossary/glossary-checklist/

Vos , R. A., Biserkov , J. V., Balech , B., Beard , N., Blissett , M., Brenninkmeijer , C., van Dooren , T., Eades , D., Gosline , G., Groom , Q. J., Hamann , T. D., Hettling , H., Hoehndorf , R., Holleman , A., Hovenkamp , P., Kelbert , P., King , D., Kirkup , D., Lammers , Y., DeMeulemeester , T., Mietchen , D., Miller , J. A., Mounce , R., Nicolson , N., Page , R., Pawlik , A., Pereira , S., Penev , L., Richards , K., Sautter , G., Shorthouse , D. P., Thtinen , M., Weiland , C., Williams , A. R. & Sierra , S.2014. Enriched biodiversity data as a resource and service.Biodiversity Data Journal2, e1125.

Wagenitz , G.2008. Wörterbuch der Botanik, Nikol.

Walls , R. L., Athreya , B., Cooper , L., Elser , J., Gandolfo , M. A., Jaiswal , P., Mungall , C. J., Preece , J., Rensing , S., Smith , B. & Stevenson , D. W.2012. Ontologies as integrative tools for plant science. American Journal of Botany99(8), 1263–1275.

Wang , P. & Xu , B.2009. An effective similarity propagation method for matching ontologies without sufficient or regular linguistic information. In The Semantic Web, Fourth Asian Conference, ASWC 2009, Shanghai, China, December 6–9, 2009. Proceedings, pp. 105–119.

Wang , P., Zhou , Y. & Xu , B.2011. Matching large ontologies based on reduction anchors. In IJCAI ’11, Proceedings of the 22nd International Joint Conference on Artificial Intelligence, Barcelona, Catalonia, Spain, July 16–22, 2011, pp. 2343–2348.

Weiland , C., Kulmanov , M., Schmidt , M. & Hoehndorf , R.2019. A machine learning based approach for similarity search on biodiversity knowledge graphs. Biodiversity Information Science and Standards3.

Whetzel , P. L., Noy , N. F., Shah , N., Alexander , P. R., Dorf , M., Fergerson , R. W., Storey , M. D., Smith , B., Chute , C. G. & Musen , M. A.2011. Bioportal: ontologies and integrated data resources at the click of a mouse. In O. Bodenreider, M. E. Martone & A. Ruttenberg, eds, Proceedings of the 2nd International Conference on Biomedical Ontology, Buffalo, NY, USA, July 26–30, 2011, CEUR Workshop Proceedings 833, CEUR-WS.org.

Wilkinson , M. D., Dumontier , M., Aalbersberg & al. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data3, 160018+.

Yilmaz , P., Kottmann , R., Field , D., Knight , R. & al. 2011. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (mixs) specifications. Nature Biotechnology29(5), 415–420.