Talk:Ontology for Investigations on Pathogenicity

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Development notes 9 July 2014

We (N and LS) went through ontology wiki pages. Comments/ suggestions

- Action Artem: write down how the wiki pages were produced. This will go to the methods section in our paper. - Wiki pages are excellent for our internal use, but we will advertise them for external users. Therefore every page needs to have sufficient information about what it is (definitions) and how it will be used and who can edit. We need to decide about editing privileges. Users should register first.

- the name of the ontology OIP (an ontology for investigations on pathogenicity): it is hard to pronounce the short name. We need to consider other names and abbreviations. For example OntoPath, IPO.

- The term “Reference” is not strictly speaking used correctly. We changed it for ‘notes’ (only for one class ‘Accession ID'), but we are not happy with it either. We need to think of a better term. - We removed [] around the reference number, again only for the class ‘Accession ID'. We hope there is a way to do it consistently everywhere. - Replace everywhere in definitions/ comments ‘is a kind of’ with ‘is a’ - Change the structure of wiki pages for ontology terms. Have an area ‘suggested definition’, ‘external references’

Definitions are required (we cannot make them): e.g. Accession ID

Definitions/ labels needs to be improved, e.g. Condition. Suggestion to use EFO term ‘experimental factor’

Disruption. Of what?

Function: replace by gene function? Inhance definition.