Integrating ecoinformatics resources on the semantic web

Parr, Cynthia; Parafiynyk, Andriy; Sachs, Joel; Ding, Li; Dornbush, S.; Finin, Tim; Wang, David; Hollander, Allan D.

doi:10.1145/1135777.1136021

Cited by 8 publications

(8 citation statements)

References 5 publications

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“…Further, recent interaction with the Environments-EOL initiative [ 51 ], which is utilising text-mining approaches to annotate Encyclopedia of Life (EOL; [ 5 ]) pages with ENVO classes, is providing valuable guidance in ENVO’s development. Further, we have worked with the ecoinformatics community to map the environmental descriptors in ENVO to the SPIRE vocabulary [ 52 ]. This allows ecological interaction data mapped to SPIRE to be re-mapped to ENVO.…”

Section: Resultsmentioning

confidence: 99%

The environment ontology: contextualising biological and biomedical entities

Buttigieg

Morrison²,

Smith³

et al. 2013

J Biomed Sem

283

193

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As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; http://www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, content, structure, adoption, and governance approach. The ontology is available from http://purl.obolibrary.org/obo/envo.owl - an OBO format version is also available by switching the file suffix to “obo”.

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Section: Resultsmentioning

confidence: 99%

The environment ontology: contextualising biological and biomedical entities

Buttigieg

Morrison²,

Smith³

et al. 2013

J Biomed Sem

283

193

View full text Add to dashboard Cite

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“…Especially in the life history and ecology domains ontology coverage is still sparse. EOL staff therefore regularly propose new terms for adoption into ontologies like PATO and CHEBI, and we are involved in efforts to extend the Relations Ontology (RO), 31 Population and Community Ontology (PCO), 32 and Biological Collections Ontology (BCO) 33 to improve coverage of the different dimensions of biotic interactions.…”

Section: Semantic Annotationmentioning

confidence: 99%

TraitBank: Practical semantics for organism attribute data

Parr

Schulz

Hammock

et al. 2016

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Abstract. Encyclopedia of Life (EOL) has developed TraitBank (http://eol.org/traitbank), a new repository for organism attribute (trait) data. TraitBank aggregates, manages and serves attribute data for organisms across the tree of life, including life history characteristics, habitats, distributions, ecological relationships and other data types. We describe how TraitBank ingests and manages these data in a way that leverages EOL's existing infrastructure and semantic annotations to facilitate reasoning across the TraitBank corpus and interoperability with other resources. We also discuss TraitBank's impact on users and collaborators and the challenges and benefits of our lightweight, scalable approach to the integration of biodiversity data.

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“…This choice of functions was based on our study of ontology tools, frameworks and services (Section 3), and of several biodiversity systems (e.g., SinBiota [13], Spire [48] or GBIF [6]). This was complemented by a process of requirements elicitation conducted with the biologists that work in WeBios.…”

Section: ) Andmentioning

confidence: 99%

“…The external repository used to test taxonomic (non-ranked) search was the Spire portal 3 [48] accessed via URI ''http://spire.umbc.edu/ont/ ethan-part.php''. Since it does not offer a WS interface, we had to implement this external access using HTTP requests, which return an OWL file.…”

Section: Implementing Aondeâmentioning

confidence: 99%