[Gmod-gene-page] Re: GMOD: Unified Gene Page working group

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Hi Don,

This is a great beginning and came in at a very appropriate time. We at 
Gramene are working on resolving some of the issues in our gene centric 
presentation strategy. I have tried to capture some of the very early 
thoughts from our side in this document at 
http://ascus.plbr.cornell.edu/~gramene/gene/template_gene_page_entry.html. 
Will be working on the updates soon.

Even before we begin, I think we need to define some of the very basic 
concepts that we are going to put together.

Thanks

Pankaj

Don Gilbert wrote:

> 
> Dear organism database folks,
> 
> One outcome of the April 04 GMOD meeting is a working group to decide if
> and how we can create a 'Unified Gene Page' for organism databases.  You
> either volunteered for this group, or were volunteered by someone else
> :)  There is no required work except that at some point each
> represented MOD will want you to vote on how to proceed with group
> recommendations.
> 
> I'm hopeful we can accomplish something this summer, and have
> suggestions/recommendations by fall 2004 GMOD meeting. Please use the
> gmo...@li... for discussion, unless there is a
> need for non-public talk. See attached doc for the background and focus
> of this group to let you better decide.
> 
> I'd suggest this to start:
> 
>   - Focus on biology now, leave computing to later.  The major need
>   is to distill biological knowledge about genes to say what
>   MODs should be representing in a common way.
> 
>   - Look over example MOD gene pages.  The approach suggested of
>   removing HTML to look at content, labels and organization struck a  chord
>   in meeting discussion.  XML-izing gene pages is not necessary,
>   but is one useful way to distill common information and structure.
> 
>   - Create a few sample unified pages, and show them
>   around for comment.  We should ask for input from gene page
>   consumers:  scientists who study a few or many genes across
>   organisms; data miners who use gene pages in bulk (academic, govt.,
>   industry, other databases).
> 
>   - Speak up if you want to actively help.   I've been working on this
>   subject since 1999 -- some one else may have better luck in a new
>   approach at consensus. If you are, or know of, someone with a strong
>   biology background who uses different MOD gene pages, interested in
>   organizing this group, please say so. Even if we decide this topic
>   should be shelved, at least we should gather evidence on why the cost
>   to unify gene pages is not worth the effort.
> 
> 
> Would you confirm if you indeed are willing to join this group, if I
> have your correct e-mail, affiliation, name, and if it is ok to add
> your name/e-mail to public documents?  If you are not the best
> person for this group, please suggest someone else at your MOD.
> 
> 
> -- Don Gilbert
> 
> 
> GMOD: Unified Gene Page Working Group
> 
> TAIR: Leonore Reiser (lr...@ac...; www.arabidopsis.org)
> GO: Suzanna Lewis  (su...@fr...; geneontology.org)
> MGI: Joel Richardson  (je...@in...; www.informatics.jax.org)
> SGD: Kara Dolinksi (dol...@pr... ; www.yeastgenome.org)
> dictyBase: Eric Just (dictybase.org)
> RGD:  Dean Pasko  (dp...@mc...; rgd.mcw.edu)
> Wormbase: Raymond Lee  (ra...@ca..., wormbase.org)
> Gramene: Pankaj Jaiswal (pj...@co...; gramene.org)
> EcoCyc/BioCyc:   Ingrid Keseler (ke...@ai...)
> Zenbase: Jeff Bowes  (bo...@uc...; www.xenbase.org)
> SGN: Lukas Mueller (la...@co...; www.sgn.cornell.edu)
> MaizeGDB: Trent Sigfried (dev...@ia...; maizegdb.org)
> FlyBase: Don Gilbert (gil...@in...; flybase.net, eugenes.org)
> 
> NOTE: need email for Eric Just (dictybase.org)
> Maybe add locuslink devs; ensembl devs; genecards devs?
> ------------------------------------------------
> 
> 
> 
> Toward a Unified Gene Page
> GMOD Gene Page Working Group
> 2 May 2004
> ------------------------------------------------
> 
> This group will discuss and propose a common gene page that model
> organism/genome database members can agree to produce in some form. All
> interested parties can contribute.
> 
> Mail list:
>   gmo...@li...
> 
> Web home:
>   http://eugenes.org/all/gene-report-examples/
>     (add gmod gene-page project)
> 
> Participants:
>   (participants from 12+ MODs to be added after confirmation ..)
> 
> 
> INTRODUCTION
> ------------------------------------------------
> There may be a long-standing desire among genome data consumers and
> producers to unify the documents describing organism genes (gene pages)
> that are provided by many model organism/genome databases (MODs).
> There remain questions of whether this desire exceeds costs of effort
> to make unified gene pages.
> 
> Discussion of common gene report web pages and software should build on
> existing expertise of MODs.  These projects have years of experience
> working with life scientists to produce gene pages that capture the
> essense of knowledge from the databases, and make it understandable and
> useful to scientists. For most MODs, the gene page is probably the most
> highly used reference document that people come to MOD web sites for. At
> FlyBase.net, these account for over a third of all calls, far surpassing
> any other single use category.
> 
> 
> PLAN
> ------------------------------------------------
> One outcome of the April 04 GMOD meeting is organization of a working
> group to decide how to proceed to reach some consensus on this topic.
> Members are drawn from several existing and new MODs, and others
> interested in unified gene pages.
> 
> These points need discussion:
>  * What are common parts of MOD gene pages?
>  * What could/should be unified?
>  * Who will benefit?  Costs?
>  * Web Reports AND/OR XML ?
> 
> Suggested starting points:
> 
>   - Focus on biology now, leave computing to later.  The major need
>   is to distill biological knowledge about genes to say what
>   MODs should be representing in a common way.
> 
>   - Look over example MOD gene pages.  The approach suggested of
>   removing HTML to look at content, labels and organization struck a  chord
>   in meeting discussion.  XML-izing gene pages is not necessary,
>   but is one useful way to distill common information and structure.
> 
>   - Create a few sample unified pages, and show them
>   around for comment.  We should ask for input from gene page
>   consumers:  scientists who study a few or many genes across
>   organisms; data miners who use gene pages in bulk (academic, govt.,
>   industry, other databases).
> 
>   - Speak up if you want to actively help.   I've been working on this
>   subject since 1999 -- some one else may have better luck in a new
>   approach at consensus. If you are, or know of, someone with a strong
>   biology background who uses different MOD gene pages, interested in
>   organizing this group, please say so. Even if we decide this topic
>   should be shelved, at least we should gather evidence on why the cost
>   to unify gene pages is not worth the effort.
> 
> As a target goal, a proposal for unified gene pages could be ready for
> GMOD meeting in Fall 2004.  There is a GMOD mailing list for discussion,
> and any documents, sample pages, and software can be deposited at
> gmod.sourceforge.net.  The euGenes.org gene page service is also
> available for such, and test cases.
> 
> 
> WORKING DOCUMENTS
> ------------------------------------------------
> We likely should create a 'gene-page' CVS project at
> gmod.sourceforge.net for documents and samples. There are example gene
> pages (see below, above), some sample extracted content (HTML -> XML).
> DGG has a preliminary 'Gene Page Scraper' that automates in Perl the
> by-hand methods I used for removing HTML styles, extracting common
> content of MOD gene pages.  Useful to gene-data-miners even if not
> otherwise, though it likely has a short lifespan as web page design
> changes will break it.
> 
> 
> BACKGROUND (MEOW/euGenes effort)
> ------------------------------------------------
> In 1999, attendees of the Model Eukaryote Organism Workshop proposed to
> develop a common set of summary gene information.  A test website grew
> out of this, produced primarily by Bill Gelbart and Don Gilbert.  This
> was produced by extracting common gene information from existing MODs
> public data. Don has continued the MEOW effort at common summary gene
> information as euGenes.org, though it never achieved the desired goal of
> having each MOD contribute common summary data.  The euGenes effort,
> without MOD contributions  or external funding, has only middling
> success at trying to maintain current gene summary pages in the face of
> effort needed to match changing genome data.
> 
> The Generic Model Organism Database project (GMOD) arose from related
> thoughts (and grant agency spurs for cost-effectiveness) that there
> should be common effort at building databases, software tools, and
> common practice methods for developing new organism databases, and
> updating existing ones. This has been an NIH funded project with many
> MOD participants, and as of 2004 is beginning to bear fruit in terms of
> commonly usable MOD components.
> 
> With many more organism genome databases coming into being in decade
> 2000, the usefulness of having common gene information and documents is
> growing, both among database providers and the many customers of these
> (from individuals to academic, government and industrial R&D labs, and
> other bioinformatics database developers). A hopeful new goal of GMOD is
> to tackle the 'Unified Gene Page' question again, with fresh perspective
> and see if a new consensus on utility
> 
> Along with MODs, there are numerous bioinformatics web/database services
> that have gene-related reports, and can offer useful insights to this
> topic.  Many of these are found as External_Links on MOD gene pages.
> Often these draw the gene summary data from MODs, in ways similar to the
> data mining MEOW/euGenes was constructed with, which is another cost of  
> having
> non-unified gene information.
> 
> 
> FIRST SUMMARY GENE PAGE PROPOSAL
> (extract of Model Eukaryote Organism Workshop, W. Gelbart, Feb. 1999
>  http://eugenes.org/docs/meow-startup.txt )
> ------------------------------------------------
> ... to establish a common interface for the major model eukaryotic
> organism databases.  This interface would be offered as the default
> homepage for nonspecialists wishing to access any of the participating
> databases. ... This home page would provide gene/gene product query
> access to based on gene symbol, gene product characteristics, chromosome
> position and perhaps homology (if we can agree on criteria to be used).
> Our view is that this will satisfy the needs of many nonspecialist users
> without forcing them to learn the intricasies and idiosyncracies of each
> of our sites. ... We had discussed a design principle that each gene
> "page" would contain no more than one screenful of information.
> Further, the gene pages should as much as possible focus on
> coin-of-the-realm molecular biological terminology rather than
> species-specific jargon.  I suggest we try to flesh out what a typical
> page would contain.  Here are some suggestions for relevant fields on
> the "gene report page", in order to get a discussion started:
> 
> *Valid terms:
>         -Gene symbol
>         -Gene full name
>         -Gene identifier number
> 
> *Synonyms:
>         -Symbol synonyms
>         -Full name synonyms
>         -Secondary gene identifier numbers
> 
> *Map location information:
>         -Chromosome and genetic map position
>         -Molecular map information (simple graphic of DNA length,
>           encoded transcript(s) and CDS(s) if available)
> 
> *Gene product information:
>         -Functional information (from function ontology if available)
>         -Structural information (from InterProt)
>         -Homology information with other "MEOW" organisms (we would
>           need to agree on some computable criteria for this field,
>           which is of course not trivial)
> 
> *Links to extended gene information in the specialty model organism DBs.
> *Brief free text gene summary (a few lines at most).
> 
> 
> APRIL 2004 OUTLINE
> ------------------------------------------------
> Example work is at
> http://eugenes.org/all/gene-report-examples/
> 
> Common gene attributes (drawn from existing MOD pages)
>  * Names, symbols/IDs, synonyms
>  * Map locations
>  * Sequences
>  * Reagents
>  * Gene ontology
>  * Similar Genes
>  * Database cross-refs, External links
>  * Alleles, Transcripts
>  * Proteins, Structure and Domains
>  * Expression and Mutant Phenotypes
>  * Gene Interactions
>  * Literature references
>  * Summary Text
> 
> Common to gene pages?
>  * Labels - are these same things?
>   -- Gene / locus / orf
>   -- Homolog / ortholog / relationship / similarity
>   -- Citation / publication / reference
>  * Organization of document
>   -- Section headers
>   -- Important at top, common ordering?
>  * Structure and size of default document
>   -- Tabular, text, document-like, ...
>   -- One screen or long report
>  * Graphics (maps, icons, ...)
>  * Further Detail options
>  * Layout and Design (colors, formatting, fonts ..)
> 
> What is customizable?
>  * MOD customizations
>   -- Look and Feel
>   -- Details & Extensions
>  * Customer choices
>   -- Best for organism community (org. standard)
>   -- Best for general reader (general standard)
>   -- Best for beginners or experts (simple,complex)
> 
> Example Gene Pages
> 
> Common Gene XML?
>  * Computable text of gene page ?
>   -- "what you see (web page) is also what your computer can read"
>   -- simple and human-readable, or complex and detailed
>  * XML variants, tabular, other?
>   -- Ace2XML, NCBI XML, others
>   -- Samples (Web -> XML)
> 
> 
> COMPARE EXISTING MOD GENE PAGES
> -----------------------------------------------------------
> For a start at gathering this common experience into a set of common
> values and practice in gene page presentation, I picked a highly
> homologous eukaryote gene Calmodulin, and pulled out gene reports on
> these from these organism databases:
>   yeast - SGD
>   arabidopsis - TAIR
>   zebrafish - ZFIN
>   worm - WormBase
>   rice - Gramene
>   human - LocusLink
>   mouse - MGI
>   rat - RGD
>   mosquito - Ensembl
>   fly - FlyBase, euGenes, LocusLink, Ensembl
>     (see same gene from different viewpoints)
> 
> There are several Calmodulin(-like) genes/org, I just used one from each
> source.  Find these at http://eugenes.org/all/gene-report-examples/
> or  ftp://eugenes.org/eugenes/gene-report-examples/
> 
> - Don Gilbert
> 
> 24 Apr 2004 - These have been updated to current versions.
> As well, four gene pages are translated from HTML to XML, for
> cut/paste/edit to design common gene pages. The XML should
> (theoretically, with right software/templates)
> allow regeneration of the original web pages.
> 
> 5 Sep 2003 - Example gene web page reports from several model
> organism databases.
> 
> URLs for the Cam gene pages (Sept 2003; updated Apr 2004 -
> alternate reports removed to focus on common summary pages)
> ---------------------------------------------------------
> 
> http://flybase.net/cgi-bin/fbidq.html?FBgn0000253
> 
> http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=S0000313
> 
> http://www.informatics.jax.org/searches/ accession_report.cgi?id=MGI:88251
> 
> http://www.arabidopsis.org/servlets/TairObject?type=locus&id=29764
> 
> http://www.wormbase.org/db/gene/gene?name=cmd-1;class=Locus
> 
> http://rgd.mcw.edu/query/query.cgi?id=2257
> 
> http://www.gramene.org/perl/protein_search?acc=P29612
> 
>   ## newly inferred zebrafish calm1a gene
> http://zfin.org/cgi-bin/ZFIN_jump?record=ZDB-GENE-030131-8308
> 
> -------- summary services -----
> 
> http://www.ensembl.org/Anopheles_gambiae/ geneview?gene=ENSANGG00000010211
> http://www.ensembl.org/Drosophila_melanogaster/geneview?gene=CG8472
> 
> http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=801
> http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=24242
> http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=36329
> http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=12313
> 
> http://bioinfo.weizmann.ac.il/cards-bin/carddisp?CALM1
> 
> http://eugenes.org/cgi-bin/moidq.html?FBgn0000253
> http://eugenes.org/cgi-bin/moidq.html?AGgn0010211
> http://eugenes.org/cgi-bin/moidq.html?HUgn0000801
> http://eugenes.org/cgi-bin/moidq.html?MGgn0000995
> http://eugenes.org/cgi-bin/moidq.html?CEgn0016585
> http://eugenes.org/cgi-bin/moidq.html?ATgn0005396
> http://eugenes.org/cgi-bin/fbidq.html?SGgn0000313
> http://eugenes.org/cgi-bin/moidq.html?ZFgn0000878
> 
> 
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- gil...@in... -- http://marmot.bio.indiana.edu/
> 

-- 
************************
Pankaj Jaiswal, PhD
G15-Bradfiled Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel: +1-607-255-3103
      +1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
************************