GOLD habitat terms

[GoogleCodeExporter]

Suggested enhancement (e.g. improved definition, new synonyms, etc.):
   Adding terms to EnvO for GOLD habitats.
  There are habitat terms that contain taxonomy and anatomy terms.

Nikos Kyrpides at GOLD sent this list of terms.

I have placed the list in a google drive spreadsheet:

  https://docs.google.com/spreadsheet/ccc?key=0Ao1hXzPMk-h-dE40WTZxZllUdWtrNVMtUzhxendMdmc#gid=0

I have begun to review the habitat terms to identify terms in EnvO, terms that 
need to be added to EnvO,
and GOLD habitat terms that are a combination of more than one ontology. 

I will continue to curate this list, in the google doc in the next few weeks.

Regards,
Lynn

Original issue reported on code.google.com by lynn.sch...@gmail.com on 11 Apr 2014 at 3:32

[GoogleCodeExporter]

Could I get edit rights to this list? I can update some of these requests.

Original comment by p.buttig...@gmail.com on 17 Mar 2015 at 1:27

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[GoogleCodeExporter]

Thanks for the access!
There seems to be a lot of convolution here (e.g. between locations, qualities, 
conditions, and environments). ENVO can only address environments and some 
conditions. PATO and GAZ should host qualities and locations resp. Also, there 
are a lot of anatomy terms here, usually with reference to some taxonomy. A 
combination of UBERON and NCBI with ENVO can be used to create the relevant 
environment terms...

Original comment by p.buttig...@gmail.com on 17 Mar 2015 at 2:37

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[GoogleCodeExporter]

Agreed,
    Although GOLD has used these terms as EnvO terms, many are not EnvO terms. While others may be new terms to add to EnvO.

Original comment by lynn.sch...@gmail.com on 17 Mar 2015 at 3:25

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[GoogleCodeExporter]

There are some good ones in there for sure :)
Are you talking to PATO for some of the more quality-like terms?

Original comment by p.buttig...@gmail.com on 17 Mar 2015 at 3:27

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[GoogleCodeExporter]

I added a couple of columns, to help better explain
how the spreadsheet was set up.
With a column showing terms that are not Envo terms,
but that could be supported with other ontologies.
And some notes, to help decipher what was intended with
the initial annotations.
  The terms follow patters, location types, anatomy, locations,
that should help simplify this long list.

I hadn't looked yet at the quality type terms. Good idea.

Original comment by lynn.sch...@gmail.com on 17 Mar 2015 at 3:42

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[GoogleCodeExporter]

It's important to remember that the qualities, conditions, etc should be
anchored to an ENVO class to prevent confusion: "polar subtidal rocky reef"
is preferable and much more informative than "polar" or "polar biome".

Original comment by p.buttig...@gmail.com on 17 Mar 2015 at 3:51

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[GoogleCodeExporter]

agreed

Original comment by lynn.sch...@gmail.com on 17 Mar 2015 at 4:06

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[cmungall]

What's the status of this? I can help automate this

In fact I already may have done this, as I scraped the list of GOLD terms from the json file on the website and aligned those - but this seems like a different list. What's its provenance?

[pbuttigieg]

@lschriml should we update this? I assume that many of these terms can still be used by the GOLD and/or GSC community.

Original GDoc here

[pbuttigieg]

Also, as there are so many, a priority list would be useful (i.e. some stats on how many genome projects are annotated with each class).