Please contribute to survey on annotations

[GoogleCodeExporter]

The Outreach WG is working on a survey to gather information on how different 
ontology developers are giving credit to other ontologies when they re-use 
terms. The ultimate aim is to harmonize practices of annnotation properties 
across OBO Foundry ontologies. The target audience is obo-discuss.

The original purpose of this survey was to help us make recommendations for 
principle 1 on how to give credit to an external ontology. However, we can use 
it to gather information on other kinds of annotations, within reason.

The draft survey is at 
https://docs.google.com/forms/d/1V2fyOdGVdUaQTqYyaez6PfLa9wQiCA2H4wF8oaVRUvs/edi
t#. 

Please post your feedback and suggestions on this issue. At this point, feel 
free to suggest any kind of question on annotations, but we may par it down 
before sending it out.

Original issue reported on code.google.com by rlwalls2...@gmail.com on 3 Feb 2015 at 5:24

[GoogleCodeExporter]

Another annotation property I concerned is how to specify one ontology term is 
equivalent to one that in the external resources including other ontologies and 
database.

I found different approaches are used. Here are some examples:
- in CLO, annotationProperty rdfs:seeAlso was used, e.g. 
http://purl.obolibrary.org/obo/CLO_0000177 (cloned cell line)
seeAlso: REO: REO_0000397 (clonal cell line)

- in REO, annotationProperty IAO_xref was used, e.g.
http://purl.obolibrary.org/obo/REO_0000397(clonal cell line)
IAO_xref: OBI:clonal cell line

- in CL and SWO (software ontology), equivalentClass was used, e.g. 
CL:cell equivalentClass GO:cell

- in CL, annotationProperty database_cross_reference was also used, e.g.
http://purl.obolibrary.org/obo/CL_0000000 (cell)
database_cross_reference: FMA:68646; KUPO:0000002; WBbt:0004017; XAO:0003012; 
GO:0005623; CALOHA:TS-2035; VHOG:0001533 

Original comment by zhengj2...@gmail.com on 3 Feb 2015 at 6:05

[GoogleCodeExporter]

I don't know if you want to ask those, but I was wondering about:
- how do you find an ontology term?
- do you rely on the definition of the term, or only the label to choose which 
term to import?

Original comment by mcour...@gmail.com on 3 Feb 2015 at 9:15

[GoogleCodeExporter]

(2) I'm not sure that non-OWL users or indeed developers will understand what 
is meant by "annotations"

In giving credit, does this mean within the OBO or OWL file or elsewhere?

(5) In terms of OBO annotation properties, I'm not aware of a good way of 
giving credit other than reusing the external id and importing the definition. 
I could be wrong though!

Original comment by batchelorc@rsc.org on 17 Feb 2015 at 3:53

[GoogleCodeExporter]

Jie - CL follows Uberon, for any OBO library ontology there are logical bridge 
axioms.

Original comment by cmung...@gmail.com on 17 Feb 2015 at 4:57

[GoogleCodeExporter]

Chris - Do you mean that the bridge axioms should be used for OBO library 
ontology terms. How about refer to terms in other resources, xref for database? 
how about other terminology? I found Drug ontology added an annotationProperty 
'has_RxCUI' to refer terms in Rxnor.

I'd like that OBO Foundry can have a policy or recommended way on it. It is 
useful when integrate data annotated using different ontologies/terminologies. 

Original comment by zhengj2...@gmail.com on 17 Feb 2015 at 7:19

[zhengj2007]

This issue was moved to information-artifact-ontology/ontology-metadata#24