Ontology

Work on semantic standards for sharing COVID-19 data. Update ontologies with COVID-19 and CoV related concepts to make knowledge machine-readable and actionable for mining, logical reasoning, etc...

Communication

• slack (#ontology)

Participants

• Robert Hoehndorf (coordinator)
• Núria Queralt Rosinach
• Yongqun "Oliver" He
• Danielle Welter
• Philippe Rocca-Serra
• Claus Weiland
• Thomas Liener
• Paul Schofield
• Susan Bello
• José Emilio Labra Gayo

Calls and Meeting details:

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date	virtual meeting venue	time 1	time 2
07.04.2020	https://kaust.zoom.us/j/148518115	9 a.m./10 a.m. (GMT/CEST)
08.04.2020	https://kaust.zoom.us/j/148518115		4pm CEST 11pm Tokyo 7am PDT
09.04.2020	https://kaust.zoom.us/j/148518115	10am CEST 5pm Tokyo 1am PDT	4pm CEST 11pm Tokyo 7am PDT
10.04.2020	https://kaust.zoom.us/j/148518115	10am CEST 5pm Tokyo 1am PDT	4pm CEST 11pm Tokyo 7am PDT
11.04.2020	https://kaust.zoom.us/j/148518115	10am CEST 5pm Tokyo 1am PDT	4pm CEST 11pm Tokyo 7am PDT

Aims

• Update relevant biomedical ontologies

Skills

• Domain experts
• Curation
• Semantics: OBO, OWL, Description Logics
• Data modeling and Linkeddata

Outcomes

• New explicit and formal specifications of concepts related to COVID-19

• patient derived sample metadata annotation profile (OBO, schema.org mapping)
• prototype file uploader with sample metadata form
• virtualBH quantitative traits and epidemiology data modeling, integrating to GA4GH PhenoPacket standard, and model graphs
• ShEx expression for sequencing samples
• Integration with Arvado test workbench: https://workbench.lugli.arvadosapi.com/collections/lugli-4zz18-z513nlpqm03hpca#Files
• Pattern-based definition/decomposition of CMO classes and integration with phenotype ontology: https://github.com/leechuck/qto

Collaborations

• Public sequence resource
• Wikidata
• FAIRDATA

Ideas

You can find and contribute to project ideas.

Ontologies for COVID-19

• Coronavirus Infectious Disease Ontology

• COVID-19 Surveillance Ontology

• SciBite Vocabularies

Ontologies including COVID-19 and related information

• Human Disease Ontology

reporting checklist:

• https://www.ebi.ac.uk/ena/submit/influenza-checklist
• ENA Influenza virus reporting standard checklist ERC000032 as json
• WHO COVID-19 CRF 23MAR2020
• CDC CRF

Symptom profile for COVID-19 patients

• Stanford Health Care Clinical observations: [BLOG POST] [DATA]