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Ontobee is a linked data server for ontologies. See: http://www.ontobee.org.
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Seek feedback on updated Ontobee cover page #74

Open yongqunh opened 8 years ago

yongqunh commented 8 years ago

Edison and I have designed and implemented a new Ontobee cover page in our beta version: http://beta.ontobee.org/

In summary, this page includes two more columns:

In the OBO column, we specify whether an ontology is in OBO or not with the following option: Note: F: Foundry, L: Library, N: Not Specified/No

The Domain column currently contains information extracted from the OBO foundry website.

In addition, in the last column of "List of terms", we added tab-delimited text download format and removed "xls" download format.

We have also added sorting function for most columns.

This format is not yet on the formal ontobee.org page yet. We would like to seek your feedback first. In about two weeks, we plan to use the new format if no more feedback/objection is received.

cmungall commented 8 years ago

On 31 Mar 2016, at 15:02, Yongqun Oliver He wrote:

Edison and I have designed and implemented a new Ontobee cover page in our beta version: http://beta.ontobee.org/

In summary, this page includes two more columns:

  • OBO
  • Domain

In the OBO column, we specify whether an ontology is in OBO or not with the following option: Note: F: Foundry, L: Library, N: Not Specified/No

Why is FBcv, IAO, and others N?

The Domain column currently contains information extracted from the OBO foundry website.

That's not one of our highest quality fields. It's not even a controlled term...

btw, Is the pipeline documented? Do you get it from the yml or the json-ld or the rdf? Useful to know and to add unit tests on obo so we don't break things for you

In addition, in the last column of "List of terms", we added tab-delimited text download format and removed "xls" download format.

Who defined the list of columns and what is the rationale?

Note you make certain assumptions like SI. For example, in CEPH you have

http://purl.obolibrary.org/obo/CEPH_0000130     hectocotylus    
http://purl.obolibrary.org/obo/CEPH_0000015     arm             The 
modified arm in males used for transferring spermatophores to the 
female. In incirrates the hectocotylus is one member of arm pair III 
while in decapodiforms frequently one or both members of arm pair IV are 
modified. Many species of coleoid cephalopods lack a hectocotylus.

In fact, hectocotylus has two named class superclasses, the other being UBERON:0008811 ! intromittent organ

it's odd you don't have a PURL / link to download the OWL

We have also added sorting function for most columns.

This format is not yet on the formal ontobee.org page yet. We would like to seek your feedback first. In about two weeks, we plan to use the new format if no more feedback/objection is received.

You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/OntoZoo/ontobee/issues/74

e4ong1031 commented 8 years ago

That's not one of our highest quality fields. It's not even a controlled term...

btw, Is the pipeline documented? Do you get it from the yml or the json-ld or the rdf? Useful to know and to add unit tests on obo so we don't break things for you

All information is retrieved from json-ld. For the domain column, we can remove it if it is currently not well-documented.

Why is FBcv, IAO, and others N?

N is defined when the ontology is not available in OBO json-ld file.

IAO is L, which is OBO Library ontologies. In terms of FBcv, the information is now updated and it is now listed as L.

Who defined the list of columns and what is the rationale?

List of terms is exactly the same as in the current Ontobee version. We only provide another download format option, which is tab-delimited text file.

I think we can create a new issue to discuss what to be included in the "List of terms"

it's odd you don't have a PURL / link to download the OWL

The PURL/Link to download OWL is actually within individual ontology page, but we can definitely to add a download button in the cover page.

e4ong1031 commented 8 years ago

We are planning to switch beta display to official Ontobee next Monday.

The link to beta version as follows: http://beta.ontobee.org/. Domain is temporarily removed from the table, and there is a legend for the OBO column.

Please let me know if you have concern before Sunday.