dash usage

[cmungall]

Hi,

Could the usage of dash in labels be homogenized (or is there a reason for having differences)? For example "T cell receptor co-receptor CD8" has_part some 'T-cell surface glycoprotein [..]'

Having or not a dash between "T" and "cell" arbitrarily, coupled with underscore or not in relations makes it very hard to write a SPARQL query; even more so if I am trying to use the Protege auto-completion feature.

Thanks, Melanie

Original comment by: mcourtot

[cmungall]

Hi Melanie,

I'm not sure why this is a request to the CL tracker as the terms you reference are Protein Ontology terms.

As for the Cell Ontology, the fact that CL terms for T cells and B cells lack hyphens was not at all an arbitrary decision. Years ago I checked Pubmed and saw that "T cell" and "B cell" were the most common usage by biologists, more common than T-cell, T lymphocyte, and T-lymphocyte, and similarly for "B cell" and its variants. Thus CL terms referring to types of T cells or B cell use the hyphenless "T cell" or "B cell" as part of the term name, and most of these terms have exact synonyms using T-cell, T lymphocyte, or T-lymphocyte, etc. That's a lot of synonyms, and we may have missed a few terms here and there; I haven't checked lately. The participants at the NIAID Cell Ontology workshop in 2008 (mostly immunologists) agreed with this editorial decision.

PRO on the other hand, utilizes UniProt names for their proteins, and UniProt has not been consistent in its usage of T cell, T-cell, etc. Nor does PRO provide the wealth of synonyms that the CL provides.

I see no reason to change the CL as we have tried to be very consistent in our non-use of the hyphen here, based as I say on the usage of actual biologists, and very pro-active in providing exact synonyms. Tools that search terms via synonyms as well as term names should have no problem finding appropriate terms using T-cell or T-lymphocyte, etc. Such tools include AmiGO and OBO-Edit, although apparently not Protege. Perhaps this could be a request to the Protege developers.

Thanks,

Alex

Original comment by: nobody

[cmungall]

Thanks Alex; sorry I didn't realize those were PRO terms. You seem to have given great thought to the issue; do you think this is something the CL developers would be willing to ask PRO, in the interest of harmonization between resources? I will check with the Protege team if there is an option to add other annotations properties to the auto-completion feature.

Original comment by: mcourtot

[cmungall]

• assigned_to: Alexander Diehl
• Group: --> GO-Cell-XP

Original comment by: nicolevasilevsky

[cmungall]

GO and CL always use "T cell" as primary label.

I believe this request is intended for PRO?

On 2 Dec 2014, at 13:06, Nicole Vasilevsky wrote:

• assigned_to: Alexander Diehl
• Group: --> GO-Cell-XP

---

\ [cell-ontology-cl-requests:#197] dash usage**

Status: open Group: GO-Cell-XP Created: Thu May 31, 2012 09:14 PM UTC by Melanie Courtot Last Updated: Thu May 31, 2012 09:14 PM UTC Owner: Alexander Diehl

Hi,

Could the usage of dash in labels be homogenized (or is there a reason for having differences)? For example "T cell receptor co-receptor CD8" has_part some 'T-cell surface glycoprotein [..]'

Having or not a dash between "T" and "cell" arbitrarily, coupled with underscore or not in relations makes it very hard to write a SPARQL query; even more so if I am trying to use the Protege auto-completion feature.

Thanks, Melanie

---

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Original comment by: cmungall

[cmungall]

• status: open --> closed-wont-fix

Original comment by: nobody

[cmungall]

That is what Alex had mentioned yes, and I did talk to Darren Natale and Cathy Wu at one of the Buffalo meetings and they had agreed on homogenizing and at least add other forms as synonyms. I’m not sure whether this did or not happen, but we worked around it in our application.

Cheers, Melanie

On Dec 2, 2014, at 10:58 PM, Chris Mungall cmungall@users.sf.net wrote:

GO and CL always use "T cell" as primary label.

I believe this request is intended for PRO?

On 2 Dec 2014, at 13:06, Nicole Vasilevsky wrote:

assigned_to: Alexander Diehl Group: --> GO-Cell-XP [cell-ontology-cl-requests:#197] dash usage

Status: open Group: GO-Cell-XP Created: Thu May 31, 2012 09:14 PM UTC by Melanie Courtot Last Updated: Thu May 31, 2012 09:14 PM UTC Owner: Alexander Diehl

Hi,

Could the usage of dash in labels be homogenized (or is there a reason for having differences)? For example "T cell receptor co-receptor CD8" has_part some 'T-cell surface glycoprotein [..]'

Having or not a dash between "T" and "cell" arbitrarily, coupled with underscore or not in relations makes it very hard to write a SPARQL query; even more so if I am trying to use the Protege auto-completion feature.

Thanks, Melanie

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/obo/cell-ontology-cl-requests/197/

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[cell-ontology-cl-requests:#197] dash usage

Status: open Group: GO-Cell-XP Created: Thu May 31, 2012 09:14 PM UTC by Melanie Courtot Last Updated: Tue Dec 02, 2014 09:06 PM UTC Owner: Alexander Diehl

Hi,

Could the usage of dash in labels be homogenized (or is there a reason for having differences)? For example "T cell receptor co-receptor CD8" has_part some 'T-cell surface glycoprotein [..]'

Having or not a dash between "T" and "cell" arbitrarily, coupled with underscore or not in relations makes it very hard to write a SPARQL query; even more so if I am trying to use the Protege auto-completion feature.

Thanks, Melanie

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/obo/cell-ontology-cl-requests/197/

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Original comment by: mcourtot