Ontology Development

[Gautamshahi]

Update the existing ontology

• [x] Prepare a list of all properties in an excel file
• [ ] Reuse the existing ontology (List is shared below)
• [ ] Get the feedback from Javad
• [ ] Get feedback from Lorenz
• [ ] Present it in the status meeting
• [ ] Make a documentation
• [ ] Finalise the ontology
• [ ] Publish the ontology(already finalised, listed below)

[Gautamshahi]

List of ontology to reuse

• [x] OMP Ontology (https://bioportal.bioontology.org/ontologies/OMP/?p=summary)
• [x] Micro Ontology http://www.obofoundry.org/ontology/micro.html
• [x] sequences, collections, time interval, ranges, controlled vocabulary(eg- list of colours, list of days, ) SKOS
• [x] cell ontology from OBO, http://www.obofoundry.org/ontology/cl.html
• [x] Taxonomy Rank https://lpsn.dsmz.de/
• [x] Unit of Measurement(uO) https://bioportal.bioontology.org/ontologies/UO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000005
• [ ] Some are structure/Cultivation may need to go for some source of process
• [x] Location---Ontology for Occurrence modelling https://spec.edmcouncil.org/fibo/ontology/FND/DatesAndTimes/Occurrences/
• [ ] Bibliography Ontology(https://bibliontology.com/)

[Gautamshahi]

List of ontology publication venue(already decided)

• [ ] BioPortal (https://bioportal.bioontology.org/)
• [ ] Obo foundry (http://www.obofoundry.org/)
• [ ] OLS at EBI (https://www.ebi.ac.uk/ols/)
• [ ] TIB (http://ontology.tib.eu/)

[Gautamshahi]

The file for term matching can be found at https://docs.google.com/spreadsheets/d/1wso3rAiNVsjLTnuAamSW327wfF23R_ttEe1kfn6jOq4/edit#gid=0&fvid=1631030923

[Gautamshahi]

Updated tables till priority 10, need to look for some terms.

[Gautamshahi]

• Show the tables with properties
• Table concept with properties/class
• link to OMP/Micro
• Mark the term whose description is not sure(use the comment in OWL(eg- Notvalidated, error))

[Gautamshahi]

The Bacdive is a static database with 1-2 minor changes through the year, so DSMZ would prefer to go with the static conversion of the relational database into KG. Also, it would be great to train their entire process of transformation of tables into triples before the end of the project.

[InquisitiveVi]

Hi Javad, Just commenting here for the development of BacDive upper ontology.

[javadch]

dev will continue on #22