Ontology

Summary/Wrapup

Metadata on samples, environments and experimental protocols

Between ontology mapping (annotation?) example

• MSV (msv:http://purl.jp/bio/11/msv) Property (skos:http://www.w3.org/2004/02/skos/core#) MIxS (mixs:http://gensc.org/ns/mixs/)

msv:expAdapterSequence skos:broadMatch mixs:adapters

• MEO (meo:http://purl.jp/bio/11/meo) Property (skos:http://www.w3.org/2004/02/skos/core#) EnvO (envo:http://purl.obolibrary.org/obo/ENVO) EnvO-label

meo:MEO_0000406 skos:exactMatch envo:ENVO_00000000

envo:ENVO_00000000 rdfs:label "geographic feature"@en

still continuing between Ontology–mapping manually...

AberOWL

Improvements

• Lots of bugfixes (Lots of new issues, too)
• Improved statistics (number of unsatisfiable classes, axioms)
  • OQuaRE stats coming Some sample statistics
• schema.org markup (classes, using https://schema.org/Class and ontologies using https://schema.org/Dataset); static pages for indexing
• Links to Bio2RDF/OpenLifeData
• Show ontology metadata

Ontologies with unsatisfiable classes in AberOWL

• PTS: 1350
• IDODEN: 16
• ONTOMA: 13
• DIAGONT: 12
• ONTODM-KDD: 10
• SOPHARM: 9
• NONRCTO: 5
• MFOEM: 4
• MF: 4
• NBO: 3
• SMASH: 2
• ONTODM-CORE: 2
• JLVO: 2
• OGSF: 1
• NEOMARK3: 1
• ENM: 1
• DINTO: 1
• AURA: 1

BioHackathon usage

Uniprot to OWL

• UniProtToOWL is still converting (not enough memory). Joint work with the orthology group will permit to link the orthology related content.

Semantic Haikuthon

• Code: https://github.com/leechuck/semantichaiku
• From DBPedia:
  • Nagasaki land
  • Japan ethnic group Chinese
  • people in Japan
• From UniProt:
  • Amyloid beta
  • protein classified with blood
  • coagulation
• A non-semantic Haiku:
  • BioHackathon
  • Building the Semantic Web
  • Each fall in Japan

Ontology

• Metadata on samples, environments and experimental protocols
  • Ontology mapping between MIxS and MSV, ENVO and MEO for INSDC submission (Hiroshi Mori, Shinya Suzuki, Takatomo Fujisawa, Okabeppu, [S Kawashima (interested)])
• Ontology metadata (like VOID, just for ontologies) [Rob H]
  • BioPortal, NBDC RDF portal etc.
• HPO Japanese translation: scraping data from papers(Elements of Morphology: Standard Terminology http://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.v149a:1/issuetoc ) and Japansese webpages at http://plaza.umin.ac.jp/p-genet/atlas/ [HiroMishima]
• Cross comparison of Drug ontologies (G. Fu)
  • Drug ontologies (relevant): ChEBI, NDFRT, NCIt, MeSH, SNOMET-CT
  • lexical comparison and instance-based comparison
  • structural, functional, and therapeutic annotations

Day 1 and 2

Ontology mapping between MIxS and MSV, ENVO and MEO for INSDC submission

Participants: Hiroshi Mori, Shinya Suzuki, Takatomo Fujisawa, Yoko Okabeppu

Progress:

MIxS ( http://wiki.gensc.org/index.php?title=MIxS) defined that ENVO annotation is required to deposit sequence data to the INSDC. http://trace.ddbj.nig.ac.jp/biosample/attribute.html?all=all#env_feature

MEO Class → ENVO Class

We will describe relations of ontology terms with SKOS mapping properties. http://www.w3.org/TR/skos-reference/#mapping

skos:closeMatch, skos:exactMatch, skos:broadMatch, skos:narrowMatch and skos:relatedMatch

not use http://www.w3.org/TR/skos-reference/#semantic-relations

ENVO entities: 1979 terms

MEO entities: 1352 terms (including synonyms = 2348 terms)

427/1979 terms were automatically mapped.

Others (1552/1979 terms) = Manual mapping...

AberOWL and stuff

• generate static HTML snapshots [done], schema.org markup [done]
• Test Konklude reasoner on AberOWL: requires update of OWLLink API to OWLAPI 4, so maybe tomorrow
• Integration with Bio2RDF/UniProt/EBI-RDF: Links to Bio2RDF now working again
• Evaluation of AberOWL ontologies: in progress [Jesualdo, Rob]
• Question answering over OWL+RDF data: queries can be expanded by AberOWL, but eval missing because endpoint is down :(

Day 3

• UniProtToOWL