GO submission form
Pankaj Jaiswal
pj37 at cornell.edu
Thu Jun 28 14:16:56 EDT 2001
From:
Leonore Reiser <lreiser at acoma.Stanford.EDU>
2:10 PM
Subject:
RE: Online Plant Ontology submission Form
To:
"Bruskiewich, Richard" <R.BRUSKIEWICH at CGIAR.ORG>
CC:
"'Pankaj Jaiswal '" <pj37 at cornell.edu>, "'Vincent Leszek '"
<Leszek at missouri.edu>,
"'Susan McCouch '" <srm4 at cornell.edu>, "'Samuel Cartinhour '"
<sc167 at cornell.edu>
Hi sorry to be getting back on this so late into - had to make a bit of a
trip away and was unavailable for a while.
I agree with all of richards points about format entry- though not sure of
afew points. IF the idea is to just suggest terms and relationships the
evidence is not required, if this is a form to submit annotations, then
yes, the evidence is absolutely necessary.
and in regard to the WWW
browsing...
the WWW browser from MGI is available and written in python- we have a
programmer here very into python who we may get to working on playing with
the MGI browser for us as part of a curation tool that would have a
similar function as far as selecting the appropriate terms, and
'automating ' the input to the database.
Brad Mars from BDGP is also working on a www browser that has a nice query
interface for searching the relationships. We spent some time talking with
him a while ago about the development of the software and I expect he
will have a release for the GO meeting.
Leonore
On Thu, 21 Jun
2001, Bruskiewich,
Richard wrote:
> Hi Pankaj,
>
> Sorry about the slow reply. My access to email since leaving for Canada on
> home leave last June 12th has been problematic. I'm currently writing to you
> from the American Midwest (Kansas State) where I'm visiting some IRRI
> collaborators (i.e. Jan Leach of Plant Pathology here). I'll be at
> U.Missouri this weekend, chatting with Leszek...
>
> Anyhow, the form generally looks really good. I just have a few simple
> comments and one difficult challenge to throw out (again):
>
> * The commentary at the head of the "Information about Contributor" is
> a bit too restrictive. You should likely decide what entry slots are
> "mandatory" and identify these with asterixes (and state that these
> and only these are mandatory). The First Name, Last Name and Email
> for sure. I think one could argue about the rest of the fields.
> Perhaps, change 'University/organisation' to 'Affiliation' and make
> this mandatory as well. For sure, *don't* make zip code and state
> mandatory since foreign entries will suffer. I guess too that it
> would not be too unreasonable to make the phone number mandatory
> (but perhaps you should not call it 'Foreign Phone' but just
> 'Telephone'). Error checking on the email address could include
> checking for the '@' character(?).
>
> * Don't expect users to 'fill out using small letters'. You can always
> coerce the text into lower, upper or title case by software.
>
> * I still don't think the entry mechanism needs to ask the user for more
> than one term at a time. The iteration (and 'stickiness' of form
> widgets) for WWW based form submissions is such that it is not too
> painful to restrict users to one at a time submissions.
>
> * Consider putting the 'GO/PO ID No' first and alongside (i.e. horizontal
> to) the 'Parent Ontology term'
>
> * We should incorporate the 'Evidence' slot. Look to the
> www.geneontology.org about the possibilities for this. Put this
> just before the 'Reference...', which BTW, I'd simplify to say
> 'Citation'.
>
> * Now comes the challenging part: there should be a way for users to
> (go to) browse for 'Parent Ontology term' and 'GO/PO ID No.' and have
> it automatically be inserted into the field of an updated form.
> You could put (a) button(s) to click to go to the browser, then
> put the resulting selection into the field of the form. I realize
> that this could be a tough programming exercise for someone, but
> I sincerely feel that this is the most essential component of the
> form, to make it truly usable. Can we at least assess the feasibility
> of doing this? What's the state of art of WWW based GO browser
> interfaces (Leonore?). I'm away from IRRI until July 9th but would
> be willing to take a look at this then, maybe getting my IRRI
> programmer to consider the feasibility of doing this (she's looking
> at the GO code base as we write, while I'm away...)
>
> Bye for now. Gotta head out for supper here.
>
> Cheers
> Richard
>
>
>
>
> -----Original Message-----
> From: Pankaj Jaiswal
> To: Leonor Reiser; Vincent Leszek; Richard Bruskiewich; Susan McCouch;
> Samuel Cartinhour
> Sent: 6/14/01 3:32 AM
> Subject: Online Plant Ontology submission Form
>
> Hi Everyone,
>
> Please have a look at the enclosed ontology submission form. I am
> expecting your valuable feedbacks. Once its finalised I am looking
> forward to host it at Gramene.
>
> file:///C|/Documents and Settings/pankaj/Desktop/PlantGO_sub.htm
> --
>
> **************************************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org http://ars-genome.cornell.edu/rice
> **************************************************************
>
> <<PlantGO_sub.htm>>
>
-------------------------------------------------------------------------------
Leonore Reiser, Ph.D. lreiser at acoma.stanford.edu
The Arabidopsis Information Resource FAX: (650) 325-6857
Carnegie Institution of Washington Tel: (650) 325-1521 ext. 311
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------
"Vincent, Leszek" wrote:
>
> Leonor Reiser <lreiser at acoma.stanford.edu>
> Subject: RE: GO accession numbers
> Date: Fri, 22 Jun 2001 16:46:20 -0500
> MIME-Version: 1.0
> X-Mailer: Internet Mail Service (5.5.2653.19)
> Content-Type: text/plain;
> charset="iso-8859-1"
>
> Hi all,
>
> I like Pankaj's approach, specifically the Plant ontology (PO) and Trait
> ontology (TO) components, because it is generic enough to encompass so many
> domains. I think I was trying to be too specific by suggesting the prefixes
> for the specific domains within PO. But clearly that's unnecessary (in fact
> probably very undesirable!). Having a browser similar to that at FlyBase for
> browsing the PO will enable folk to locate their area of interest without
> having a myriad of prefixes to comprehend.
>
> I'm having some difficulty accommodating Fungal ontology within Plant
> ontology (raises taxonomic questions! & it may be 'politically incorrect?).
> The algal ontology too might need looking further. I need to review the
> current perspectives on Kingdoms etc.
>
> I was wondering if the Trait ontology (TO) format would be adequate for the
> traits of all possible taxa - but pondering this further I think it would
> work.
>
> So, according to Pankaj's scheme we would recommend just two prefixes - PO &
> TO - am I understanding this correctly??
>
> I'll stew on this over the w/end but I think it will work.
>
> I look forward to 'hearing' what others think.
>
> Regards,
> - Leszek
> xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> P. Leszek D. Vincent Ph.D., FLS
> Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573)
> 884-3716 (Agronomy), Fax:(573) 884-7850;
> Ph/Fax (Home): (573) 441-1228;
> Email: Leszek at missouri.edu
> Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> (http://www.cafnr.missouri.edu/mmp/ and http://www.agron.missouri.edu/)
> xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
>
> > -----Original Message-----
> > From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> > Sent: Friday, June 22, 2001 1:41 PM
> > To: gramene at brie.cshl.org; Vincent Leszek; Richard Bruskiewich; Leonor
> > Reiser
> > Subject: Re: GO accession numbers
> >
> >
> > Hi everyone,
> >
> > Please have a look at the follwoing scheme text: I am suggesting this
> > format. This way we can remain more generic, by
> > not being too strict with the individual plant categories. for the
> > anatomical and morphological terms, as everyone
> > knows that we have a choice of having plant anatomy/anatomy, as a more
> > generic one or if one really prefers
> > can be more specific. However the difference is not much.
> > Eventually we
> > will come across similar child-parent
> > relationships. I am open to that category, which ever way one
> > wants. the
> > terms will not be that many in number
> > that we can't fit everything under PO IDs with 0-9999999. traits TO i
> > would like them once again to be more
> > generic and can go under TO. no need to extrapolate into PTO etc. you
> > will notice chemical (CO and clinical KO
> > ontology thing in the picture. well this is just for the
> > future because
> > at some point chemists and clinician(already
> > there with human genone) would be interested in joining. For teh fly i
> > would even suggest that
> > theer should be one Animal_ontology AO and fly should be
> > there under the
> > phyla representing the insects (and
> > not as FB). Well i should not to say much about animals, but as far as
> > possible i intend to be more generic for
> > plants atleast and stick to the classical way of presenting the terms
> > rather than experimenting in a new way
> > (sometimes its good also). What do you guys say?
> >
> > -thanks
> > pankaj
> >
> > ps:For the gramene project people, This is not the final word. the
> > matter is still under discussion!
> >
> > here is the scheme:
> >
> > $Ontology ;
> > %Chemical_ontology (CO) ;
> > %elements ;
> > %molecules ;
> > %inorganic ;
> > %organic ;
> > %Clinical_ontology (KO) ;
> > %Gene 0ntology (GO) ;
> > %Biological function ;
> > %cellular component ;
> > %molecular function ;
> > %Plant ontology (PO) ;
> > %algal_ontology ;
> > %angiosperms_ontology ;
> > %Dicot_ontology ;
> > %dicot_anatomy ;
> > %root ;
> > %shoot ;
> > %dicot_morphology ;
> > %root ;
> > %shoot ;
> > %Monocot_ontology ;
> > %monocot_anatomy ;
> > %root ;
> > %shoot ;
> > %monocot_morphology ;
> > %root ;
> > %shoot ;
> > %bryophyte_ontology ;
> > %Fungal_ontology ;
> > %Gymnosperm_ontology ;
> > %Pteridophyte_ontology ;
> > %Trait_ontology (TO) ;
> > %genetic trait_ontology ;
> > %plant genetic trait_ontology ;
> > %agronomic traits_ontology ;
> > %Plant Morphological traits_ontology ;
> >
> >
> >
> >
> >
> > "Vincent, Leszek" wrote:
> >
> > "Vincent, Leszek" <Leszek at missouri.edu>,Leonor Reiser
> > <lreiser at acoma.stanford.edu>
> > Subject: RE: [Fwd: Re: GO accession numbers]
> > Date: Fri, 22 Jun 2001 09:50:26 -0500
> > MIME-Version: 1.0
> > X-Mailer: Internet Mail Service (5.5.2653.19)
> > Content-Type: text/plain;
> > charset="iso-8859-1"
> >
> > Hi folk
> >
> > Here's my briefly considered suggestion. I think it would be useful
> > for us
> > to have a prefix which includes an identifier for the
> > relevant taxon
> > (monocot & dicot) & another identifier for the specific domain that
> > the
> > prefix encompases.
> >
> > For the taxon identifier I suggest we use M for monocot & D
> > for Dicot
> > (not
> > very original but botanically pretty useful) (If/when we get to
> > include
> > gymnosperm, pteridophyte folk etc. I think there will be room even
> > then to
> > use a single letter identifier e.g. G for gymnosperm, P for
> > pteridophytes -
> > but that's looking way ahead perhaps).
> >
> > For the domain identifier - here's the list that I think is
> > relevant
> > (hopefully I haven't left out one): Developmental, Anatomy,
> > Morphology,
> > Phenotype, Trait. If we use the 1st letter of each & combine it with
> > the
> > taxon identifier we would get the following:
> >
> > MD - monocot developmental
> > MA - monocot anatomy
> > MM - monocot morphology
> > MT - monocot trait
> > MP - monocot phenotype
> >
> > DD - dicot developmental
> > DA - dicot anatomy
> > DM - dicot morphology
> > DT - dicot trait
> > DP - dicot phenotype
> >
> > I think the taxon identifiers & domain identifiers will ring good
> > 'bells'
> > with non-ontologists interested in our activities/joining
> > in. I think
> > they're reasonably understandable & carry enough info. to enable one
> > to
> > understand the coverage of each prefix. These are just my thoughts &
> > I'm not
> > wanting to be presciptive. Let's see what the rest of us suggest
> > before we
> > get back to Suzie & Lincoln. (PS I was thinking of
> > discussing this at
> > the
> > Bar Harbor meeting but there's no time like the present).
> >
> > - Leszek
> >
> >
> >
> > Lincoln Stein wrote:
> >
> > Hi Folks,
> >
> > The GO consortium thinks we should make up a prefix for the
> > phenotype
> > terms and let them know. So please send Suzi Lewis the prefix(es)
> > when you've chosen them.
> >
> > Lincoln
> >
> > Suzanna Lewis writes:
> > > >
> > > > My monocot database group is happily creating ontologies for
> > plant
> > > > traits and anatomies. Your group has been great at helping us
> > get the
> > > > ontology editor up and running.
> > > >
> > > > A question: when we create these parallel ontologies,
> > what prefix
> > > > should we use for the accession numbers? Should we make one up
> > and
> > > > tell you what it is later?
> > > >
> > >
> > > I think that is best. Pavel Tomancak here in Berkeley is doing
> > > something similar for the fly anatomy and developmental stages.
> > For
> > > these we are using the FB identifiers and I think this
> > situation is
> > > analogous.
> > >
> > > -S
> >
> > --
> >
> > ==============================================================
> > ==========
> > Lincoln D. Stein Cold Spring Harbor
> > Laboratory
> > lstein at cshl.org Cold
> > Spring Harbor,
> > NY
> >
> > NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS.
> > PLEASE WRITE FOR DETAILS.
> >
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