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Re: Meetings

wac 18 Apr 2007 23:21
in discussion PhD Project / Progress » Meetings

Meeting with Raphael

• look at NLP
• Jenny Bryan/Jochen work on hierarchical clustering may be of interest
• contingency tables - lots of work
• In addition to Disease/Brain Disease, or Brain Disease/Subgroup, also think orthogonal groups - cancer/Disease, etc.
• Worry about sequential testing
• Bayesian Statistics Book:
  • Gelman, Rubin. Bayesian Data Analysis
• NOT Available:
  • June 24th-27th
  • June 30th-Jul 8th
  • Jul 14th- Aug 7th

Re: Meetings

wac 18 Apr 2007 23:17
in discussion PhD Project / Progress » Meetings

Supervisor Meeting, April 17 2007

• Discussed CGDN Poster
  • mainly geneticists
  • target is the 3 minute spiel
  • prepare half-sheet contact info/results

• Work on statistics
• Do Venn Diagram explanations/bar charts/graphs
• Start preparing for committee meeting and exams

• worry about lack of annotated information
  • look for alternative data sources , esp gene to papers

Re: Updates

wac 18 Apr 2007 20:23
in discussion PhD Project / Progress » Updates

• CGDN Poster is now completed and uploaded
• Met with Raphael and clarified the statistics
• Preparing poster handout and working on long/short versions of the proposal

• Related articles imported (2.9 GB txt file!)
• computing related articles/term pairs
• start computing stats

• do statistics reading
• do TF/brain disease reading

Re: Updates

wac 30 Mar 2007 22:12
in discussion PhD Project / Progress » Updates

• Didn't get MSFHR (but Ryan Morin did :)
• Confirming future meeting times with Vanessa and Dora (oops, last meeting was the last one scheduled) - we could meet during CGDN worst case discussing in front of the poster
• need to start booking the qualifying exam - I do the coordination, the guidelines say 2 members + supervisor attend, so looks like I'm good in terms of number of people. Getting everyone in the same room…
  • potentially move up the qual. to first half of June (before CBW)
• migrating work environment to watson (cluster) SunGridEngine
• sonoma account made, will start loading soon
• starting to make reference list in Connotea.org

Re: Meetings

wac 28 Mar 2007 23:55
in discussion PhD Project / Progress » Meetings

Committee Meeting

• Angie will be coming from Richmond, book May 2 at 2006 CMMT (check with Dora)

Qualifying Examination

• confirm members for examination
• may need a third member - Art Cherkasov
• will be the first QE for the BITP

PubMed

• Ask Jon about pre-existing Pubmed database loads
• Ask Pavlidis Lab (Leon) re: their db load
• Ask Jon before loading on sonoma

GeneRIF graph

• separate data without Interaction GeneRIFs

SNOMED

• keep in mind, but avoid "possibly unpublishable" linkage

• Monitor Disk usage
• NB Medline ID and PMID are different - get both

Proposal

• more of a detailed outline - NOT a thesis
• shorter is better - aim for 25 pages TOTAL (with figs, refs)
• Show the "Flag markers" for the "claim of expertise"

Recent Work

• Pubmed MyNCBI, Pubcrawler - keep track of recent relevant papers

• start looking for a qualifying exam date (Dora, Vanessa, etc.)
• likely Mon or Fri in early July

Re: Agenda

wac 26 Mar 2007 21:46
in discussion PhD Project / Progress » Agenda

Committee Status and Timeline

• All members onboard (Raphael Gottardo, Angela Brooks-Wilson)
• Committee Meeting
  • All members replied: May 2 or 9
• Qualifying exam
  • recommend July 15th, hard deadline Aug. 31st - only one chance
  • Committee meeting must occur one month prior
  • Assembling Qual. Exam Committee members?

Scholarships

• NSERC PGSD3
• MSFHR (Mar 30@4)

Conferences

• CGDN
  • Abstract submitted
• ISBI
  • Poster done
  • accomodations in DC?
• Passport

CSCBC

• potential host for 2008 or 2009 (competing with UofT)

Research

Archival

• HGNC downloaded
• MeSH downloaded
• XML includes creation dates, update dates for all fields

Programming

• geneRIF histogram
  • Interaction DBs are counted as GeneRIFs
• No gene synonym generation in PubMed Searches?
• No PubMed to sequence links (reverse exists)

Re: Meetings

wac 26 Mar 2007 21:38
in discussion PhD Project / Progress » Meetings

Committee

• E-mail Angie (cc Francis and Wyeth) regarding committee member position
• Re: Angie - potential others if she is too busy
  • look for biologist
  • Marco Marra (likely v. busy)
  • Carolyn Brown
  • Matt Lawrence (chromatin)
  • Sam Aparicio
    • internal medicine, stem cell pathways
• watch for upcoming seminars, look at recent papers

Timeline

• double-check upcoming committee meeting/exam dates with Sharon

Research

• CISTI ~= Pubmed central Canadian equivalent
  • (Medical) libraries, journals
• cancer - neoplasm
  • very different, may wish to filter out or handle separately
  • may want to consider handling different diseases/disease classes separately
• See if there are links from PubMed to Sequences
• make histogram of # of GeneRIFs
• PubMed gene synonym handling
  • PubMed-gene link histogram
• NLM MeSH handling
  • look at Protégé (Stuart), AmiGO
  • ontology browsers
• Freeze the HGNC (download)
  • HUGO - identified proteins
  • 18,000 genes with names
  • 6000 "unknown"
• Genetic Disease database
  • gene tests/risk databases (Sid for ref from Alzheimer paper)
• Looking into housing PubMed
• inquire with Jonathan Lim regarding disk usage, setting up dbs

Re: Updates

wac 24 Mar 2007 22:22
in discussion PhD Project / Progress » Updates

Confirmed: I got offered the NSERC Postgraduate Scholarships D - 3 years (PGS D3)!
The research-results page now has a histogram of the number of GeneRIFs per gene.

Re: Updates

wac 23 Mar 2007 02:51
in discussion PhD Project / Progress » Updates

• XML parsing is no more fun than the last time
  • resulting XML files are LARGE - 1/2 meg per gene or more
  • implemented a "stream-based" parser so minimal memory used (limited by download speed)
• Extracted list of Gene Ids and counted number of GeneRIFs, PubMedIDs for the geneRIFs
  • each GeneRIF may have multiple PubMed Ids
  • links to interaction databases are also considered GeneRIFs
  • Entrez gene has creation and update dates for all the GeneRIFs

Re: Updates

wac 20 Mar 2007 21:34
in discussion PhD Project / Progress » Updates

• cgdn-poster-abstract "release candidate" complete - due March 26
• started programming Entrez EUtils parser in Icon

Re: Updates

wac 12 Mar 2007 21:44
in discussion PhD Project / Progress » Updates

• SnoMED CT does allow for free use for research purposes as part of the UMLS
• Angie agreed to become a committee member!

Agenda

wac 06 Mar 2007 07:01
in discussion PhD Project / Progress » Agenda

• Fourth Committee Member
• Disease Terminologies
• Data storage and Computation Resources
• Timeline

Updates

wac 06 Mar 2007 06:45
in discussion PhD Project / Progress » Updates

Current Updates placed in Research Results

• Disease Terminologies: MeSH, ICD, SNOMED CT
• EUtils query examples to download needed data from NCBI
• Basic Data Model Diagram

Meetings

wac 20 Feb 2007 23:06
in discussion PhD Project / Progress » Meetings

Mon Feb 19 2007 Meeting:

Disease source

• Question: What is a disease
• Hold OMIM out as a verification source
• look for resource describing diseases
  • if general reference not available, try specific disease reference
  • compare to commercial tools
  • discuss with semantic web people - Ben Good, Mark Wilkinson

• Check on Simon Twigger (U. Wisc.)
• Neuronames
  • find out how widely used
• implementation: NCBI E-Utils

To-Do Items

1. transcription factor genes from Entrez Gene
2. Neuroname brain disease publications from PubMed
3. MeSH brain disease publications from PubMed
4. GeneRIF (gene,pubmedID)
5. Link Disease to PubMed (find resource?)
6. Link TF Genes to Disease via PubMed

• Reading: Robbins Pathology textbook