Summary of discussion

[Pankaj Jaiswal]

Hi Everyone,

My comments follow Leszek's.

"Vincent, Leszek" wrote:
> 
> Hi colleagues
> 
> Here's a summary of the items discussed during our phone conference last week (05/07/'02) - not presented in order of importance or chronological order:
> 
> 1. Development of a site-neutral ontology browser - Pankaj mentioned that this is to be developed in the near future (during the next few weeks?).
> 
It is going to be the same browser we have it on Gramene. However for POC web
site, the browser and the Ontology DB will be independently hosted for POC 

> 2. Possibility of a phenotype workshop & small POC meeting after the ISMB meeting in Canada - with Richard B. & Michael A. Most folk would be otherwise occupied at this time (& not attending the ISMB meeting) & so would not be available to attend. Reaffirmed the useful role of phone dialogue as a stop-gap.
> 
Michael, Suzi Lewis, Judith Blake, Susan and myself had a discussion on Sunday
05/12/2002 about this workshop. The outcome was instead of holding it at ISMB,
where not many of us will go, it was suggested that we will hold this 2 day
workshop somewhere on East coast (US), possibly on 19-20th Oct'2002.
Representatives from MGI, TAIR, FlyBase, Wormbase, RatGD, SGD, Gramene and
others (about 20-25 people), will attend and comeup with a resolution on how are
we going to curate the phenotypes. More details will follow from Michael, once
he finalizes the dates.


> 3. Comments on Temporal ontology:
> - consider providing more explicit wording for Root;

I do not understand, what root are you talking about Root the term or the Root
in DAG.
> 
> - consider providing the scientific name for each taxon referred to - species name if possible but at least generic name. This would facilitate users of ontology using taxon-appropriate controlled vocabulary because taxa would be identified by internationally recognized scientific names (according to the  international code of botanical nomenclature (ICBN) principles). Common name can be retained to facilitate recognition - e.g. arabidopsis (Arabidopsis thaliana Heynh.) & sorghum (Sorghum bicolor (L.) Moench.). This would also contribute to credibility of ontology information. Furthermore, it would enable users to discriminate between closely associated taxa such as S. bicolor & S. propinquum which might be separately referenced in our ontologies, in time;

I don't think the workers studying Arabidopsis neglecta or Arabidopsis thaliana 
or someone working on O.sativa Vs O.glaberrima, or S.bicolor Vs S.propinquum
will spell out different growth stages. Infact the zadoc scores mentioned in the
file I sent you were common for Wheat, barley and oat. So i don't think we
should get into such details of taxonomy. If one really intends to have it then
mentioning this info in definition or the comments field will suffice. I might
be wrong in visualizing this fact so please correct me.

> 
> - Consider standardizing the citing of curatorship info. Currently the format is 'GR:pj37'. Consider 'Curator:Gramene,pj37'. Subsequent comment has been that curatorship info. need only be provided where published term definitions are modified by a curator. The latter is a less-tedious route;
> 
This is something POC has to communicate with GO. Reason our Ontology DB is in
concordance with the GODB. Either way its fine with me.

> - 'PMID' used in Dbxrefs - consider using 'PUBMED' as in list of acceptable abbreviations;
> 

Not possible. 'PMID' is the preferred identifier as mentioned in GO DBXref. We
use the same.


> - The printed reference info. should be provided in the first instance. Where a URL can be cited for a term definition this should not be used in place of the printed source but can be used in addition to the printed source.

Somebody has to go through the published literature, but given the time and
resources, we have at the moment in Gramene, it is not possible for us to
undertake the exercise at the moment. However, if we come across a more
appropriate definition during the course of our annotation, we will update the
existing definition/synonym and DBXref. I don't know about TAIR, IRRI and
MaizeDB so please bear with me. Another option would be to contact some
scientist/interested person, who can peer review the PO terms and provide
definitions.
> 
> 4. Leonore would email a copy of the scanned glossary file from Esau (Anatomy of Seed Plants) - around the > group. 

I have it and use it for my terms.
> 
> 5. Noted that significant problems existed in the anatomy ontology which comprised the TAIR anatomy ontology 'merged' with some Gramene ontology......
> 
I am trying to fix most of the suggestions that came from TAIR. Please feel free
to send in your suggestions and comments.

> 6. Noted that the Temporal ontology (Development/Growth) presented a dicot / monocot dichotomy which was undesirable. Preferable to have dicot / monocot affinities emerge later in the ontologies (if at all?). Is it necessary to cite this dicot / monocot perspective?? The means by which we represent dicot / monocot associations (if desired) will need some puzzling over. Noted some confusion between these taxon-specific ontologies & the desire to produce a generic ontology which leads to taxon-specific ontologies (I think that's what I perceived or did I get that wrong??).
> 
> [Post-meeting comments: what's the intention of the Temporal ontology - generic or taxon-specific or both?? If it is intended to be generic, in the non-taxonomic sense, and taxon-specific, then it would seem that "sensu ..taxon name.." would need to be used for all the taxon-specific info. At present, taxon-specific ontologies are presented].
> 


I will work on this over the next week and then seek your suggestions.

> 7. Regarding the 'merged' anatomy ontology - Noted some significant points:
> a) parent-child 'lineages' need to be tested for adherence to the True Path Rule (http://www.geneontology.org/doc/GO.usage.html);
> 
> b) affirmed that testing for adherence to the True Path Rule (TPR) is time consuming & necessitates considerable application & interpretation of basic botanical (& biological) anatomical 'systems';
> 
> c) affirmed that it is essential that the content of all of our ontologies be rigorously tested for adherence to the TPR so as to ensure scientific accuracy of the content. This is a very time consuming task but is unavoidable if we are to gain the confidence of potential users of POC ontology products;
> 

Sure, I am going through them personally, but to cross check everyone else
should also go through it and send in their comments.

> d) suggested that ontologies should not be publicly available until each is considered to mirror the current understanding of botanical knowledge domains e.g. anatomy, temporal (development/growth) & have been tested for adherence to the TPR;

Ask for Peer reviewing them

> 
> e) noted that the anatomy ontology had some word substitutions - different words associated with the same definition (I think we referred to this as 'word duplications' during the ph.call) - consistency needs to be achieved here;
> 

fixing them.


> f) certain words were used as terms & not as synonyms;
> 

please point them and send it to me


> g) noted that some of the original TAIR definitions had been improperly treated ('partially corrupted');
> 
> h) suggested that the "Commit" & "Commit as New Term" buttons were not being consistently used & that perhaps this had contributed to the corruption noted;
> Quite a chance, will try to be more consistent from my side.

> i) decided that we would consider how to correct the anatomy ontology that Pankaj had developed - either by Pankaj re-developing the ontology, by building it on the TAIR's anatomy ontology, or by us all evaluating the anatomy ontology & passing on comments to Pankaj.

Try to go through the file I will send you in a few days. If it does not work
then build a new one.

> 
> [My 'take' on this is that the original developer would hopefully do the redeveloping. Once the difficulties cited in paragraphs e, f, g & h above have been resolved the rest of us should get involved with testing for adherence to the TPR - either by us each reviewing the entire structure or by division of the structure for testing of components amongst us. My preference would be for us each (or as many as possible of us) to check the entire structure for TPR adherence. Either way this will be tedious but I think that's what putting together an excellent product will take].

Could you please send in all your comments by monday, so that i can work on
them.
> 
> 8. Some other points which I think I raised:
> - DAG-Edit arranges terms in alphabetic & numerical order - it would be important to avoid this style of arrangement in browser views i.e. 'children' under a 'parent' should be arranged in a biologically meaningful order. Pankaj thought this could be achieved via the browser s/ware (I hope so as this biologically meaningful ordering of terms will probably be anticipated by most users of our ontologies);
> 

Not a priority at the moment.

> - Developmental stages of Zea need to include 'milk stage' (maizeDB ID# 67373);
> 

I checked it just now, its already there.

> - the word 'wither' in TAIR-based ontology could be associated with the word 'senesce';
> 
Done

> - typos in some of the TAIR-based definitions;
> 

I will pass the files through spell check.
> - Dbxrefs for some synonyms are missing;
> 
Somebody has to go through them. At the moment all the DBXrefs are associated
with Definitions.

> - some text absent for some synonyms e.g. for V12-V14 for Zea;
Please correct it. Its maize.

> 
> - consider citing the URL for the online medical dictionary for term definitions (secondary reference). The URL is: http://cancerweb.ncl.ac.uk/omd/index.html
> 
> 9. Leszek mentioned that he hoped to be able to resubmit a proposal to the NSF for funding for the POC.
> 
> Subsequent news is that the perceived hurdles on the UM-C campus have been overcome & I've been approved to serve as PI on this proposal. The 'wheels' are already in motion...
> 

Great news. Good luck !

> How can you contribute to this proposal?? Should you have some 'gut' or considered feedback based on last year's submission then please don't hesitate to share it with me (I can resupply you with a copy of the previous proposal).
> 

> 

Pankaj