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Cellosaurus - a controlled vocabulary of cell lines #62

Closed vedina closed 8 years ago

vedina commented 8 years ago

I was not aware of this resource - is the content the same as cell line ontologies ?

Cellosaurus - a controlled vocabulary of cell lines http://web.expasy.org/cellosaurus/

fehrhart commented 8 years ago

I had a look at it and for me it looks like an online dictionary for cell lines. They try to implement a(nother) code for each cell line including modified clones. It contains more information, more details and more cell lines as the ontology - e.g. I found 65 different varieties of Jurkat cells in cellosaurus and 4 in the cell line ontology. It has a search function but no (visible) structure. I also cannot filter for species or browse - only search. So for getting information about a cell line it is very well done and informative.

On 30 April 2016 at 08:31, Nina Jeliazkova notifications@github.com wrote:

I was not aware of this resource - is the content the same as cell line ontologies ?

Cellosaurus - a controlled vocabulary of cell lines http://web.expasy.org/cellosaurus/

— You are receiving this because you were assigned. Reply to this email directly or view it on GitHub https://github.com/enanomapper/ontologies/issues/62

AmosBairoch commented 8 years ago

The full description of the Cellosaurus is here: http://web.expasy.org/cellosaurus/description.html In addition to the ASCI and OBO format, there will soon be an XML version. The next release (19) will be in a couple of weeks.

egonw commented 8 years ago

@AmosBairoch, will there also be an OWL version?

AmosBairoch commented 8 years ago

On 27.09.2016 12:17, Egon Willighagen 0000-0001-7542-0286 wrote:

@AmosBairoch https://github.com/AmosBairoch, will there also be an OWL version?

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Hi,

For the moment it is not planned as many of the new fields (STR markers for example)make the Cellosaurus a knowledge resource far wider in scope than a OWL-based resource. I am not sure how I could model all the data that there is now in the Cellosaurus in OWL.

The next step is to have an XML version and this will be available to beta test (if you are interested) in a few weeks and in production in release 20 in october or november.

After that maybe I could see how a "slim down" version of the Cellosaurus could be distributed in OWL as a reformat of the OBO version using the OBOConverter (which a few people are already using to convert the OBO file).

Best Amos

Professor and Director of the Dept. of Human Protein Sciences at the Faculty of Medicine of the University of Geneva Group leader at the SIB - Swiss Institute of Bioinformatics

Preferred email: ab@sib.swiss

Alternative email: amos.bairoch@unige.ch

egonw commented 8 years ago

OK, clear. Then I'll close this issue for now, as our ontology building process depends on OWL versions.