HCLSIG/PharmaOntology/Meetings/2011-03-10 Conference Call/minutes
Joanne's presentation at AMIA http://www.slideshare.net/joanneluciano/the-translational-medicine
Michel: Two paths: 1) Analysis of formal SNP representation
... https://docs.google.com/present/edit?id=dc9qc59t_100g9rrbcfb&authkey=CKXAsvMI
... SO-PHARM presentsGenotype and isEnrolledIn are relations not RO
... Pharmacogenomics Ontology, still a bit underspecified
... PO is using the limited set of relations
matthias_samwald information about the SNP in the example on slide 12: http://www.snpedia.com/index.php/Rs1142345
michel http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=1142345
Matthias would like to model demyelinised patient w. more about demyelinisation
Matthias and Michel discussing whether SNP can have multiple valid alleles
Scott: Should have a layer of reasoning to make judgement calls, like excessive bleeding
... model should not have classifications embedded in
Michel: Yes, we can take all these back to measurements of some kind
Scott: Do we need a relation for biomarker?
Michel: SIO and TMO are closely aligned, in how they would represent
... want to avoid IAO handling of numbers and relationships
... Example: comments on sequence ontology, using IAO
... OBI uses IAO and SO, conforming to a common representation
Scott: Helpful to know how we are branching off
... if we can align w. OBI, etc?
Michel: We can provide an alternative view to model
... OBI would have the closest thing to a test.
Trish: comments on OBI development
Michel: Our group is trying to re-formalize some of this
... we represent entire organisms w.SIO, all fits together nicely
... we can argue that many groups have not done the representation quite right
... and we can offer our own use cases
Scott: IO Informatics, kidney transplant data, kidney cancer patients
... We need some data.
... or can we get rolling w/o data? Just construct queries?
Michel: MGI has tables of genes, phenotypes; not quite patients, but correspondences
... we are working to integrate diff genotypes across model organisms
... can look at sequence homology
... maybe find corresponding pharmacogenomic experiments
... If looking for specific patients, it's tougher to find. Patient-to-patient cohorts in actual trials
Scott: Transplant organ rejection as an AE; there are biomarker data
... but a real use case would help to move things along.
Michel: Use case scenarios are really sentences, so to force us to marshal data.
... but finding real data is hard
Michel: Paper on bioontologies is on yeast, but maybe can also do on mouse
Scott: looking at MGI site, phenotypes for cancer etc
michel http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=humanDisease&key=847478
michel http://www.informatics.jax.org/searches/allele_report.cgi?_Marker_key=24690&int:_Set_key=847156
Pharmacogenomics on mice does not present patient privacy concerns