Anatomy Ontology Conf calls

• Dial-in Number: 800.505.4464, participant passcode 784002#
• Adobe Connect: http://dukeuniversity.acrobat.com/phenoscape

June 13, 2011

Participating: Monte Westerfield, Paula Mabee, Judy Blake, Aaron Zorn, Jeff Bowes, Wasila Dahdul, Jim Balhoff

Agenda

• Judy:
  • Discussion on how to initiate the Amniote Anatomy Ontology for terms outside skeletal system
  • Report on status of unified anatomy [emap + MA]
  • What exactly is abstract mouse?
  • Clone MA, UBERON, unified mouse [emap + MA], or abstract mouse?
• Monte:
  • Discussion on moving ZFA to GO like model; possibility of implementing VAO import (so that XAO can just clone this VAO chunk when they also clone the rest of ZFA)
• Aaron and Jeff:
  • Discussion on setting up modular ontology model and specifics of importing model species-specific information (like devo stage)

Minutes

• Wasila will demonstrate diffs between Uberon and MA usingnon-skeletal terms
  • e.g. 'naris' in mouse is 'part of nose'
  • e.g. 'naris' in uberon with lots of xrefs but missing relationship 'part of' olfactory apparatus
  • not sure how often Chris updates Uberon
• Terry - developed adult Mouse Anatomy; working with Edinburgh group to update their ontology
  • 'unified mouse anatomy' not an official term, just a descriptor
  • Ed. developmental mouse anatomy developed 15 years ago in an effort to code mouse expressiondata. Built along lines of an atlas by kauffman and baird; partonomy; Used for expression annotation by ... for years now. Two parts: abstract mouse which is a time -inedpent collection of terms in a hierarhy not a dag; and from that extracted stage-dependent hierarchies. stage 28 is postnatal -- this is not developed at all. 8-10 years ago, a postnatal developed by jax. jax added is-a and expanded on stages. Examined all relevant ontologies in updating. Two entities (MA vs. developmental) not connected currently -- working to make it an anatomy ontology encompassing the whole of mouse development.
  • Q: re: timeline? Terry: within next two weeks could give clearer answer.
  • would like to work with rest of ao community to make it a resource that will best serve needs of community. It works for expression and for phenotype, but needs to work better for other communities. Have updated based on other working groups. Would like to work to update weak points.
  • Judy - Terry funded for small portion of time on issues relevant to project
  • Wasila - use mouse
  • Judy -- start with MA, great place to start. Talk with Chris to see where he last updated and worked with it.
  • Terry -- Uberon - made an effort to take into consideration only things that are shared - not less valuable for it; structurally less consistent than mouse; mouse is lacking becuase of roots in ed anatomy and purpose for expression -- so the high level structure is a partonomy; first level division into regions, then into organ systems, etc. Need to think about primary goals of new ontology. Where along tree does it no longer serve amniotes or chickens?
  • Some avian terms are already in uberon -- use mixed approach. Also uberon follows more of a is_a approach;
  • MA, Uberon, VAO, AmAO are all separate right now; good documentation of proposed changes;
• Judy: suggestion -- all work together on one aspect at a time - start with limb/fin
• Terry: Historically for MA, when significant changes made, to a section in response to some input; not a constant stream of changes; structurally and in terms of big picture, not changes often. Need to do in coordination.
• Wasila: Conclude -- need mixed approach

• Monte:
  • Need to improve ways of synchronizing zfish ontology with vao, uberon, etc. Met with db admins etc. to discuss future re: ontologies and new mechanism to stay in synch. Potential problem is that lead curator out on maternity leave, so people he discussed it with not necessarily in charge, but they understood basic issue. Charge to the zfin group (from Monte) is to write up plan and potential problems. Briefly -- problem how to grow two ontologies grow in synch. Big concern that curators have is if they become dependent on outside group such as Phenoscape, there could be changes made without consideration for the implications of zfin. Also, term request brokerage rights need to be grant to zfin. Need to work out sop for how updates are made.
  • Concern how we represent developmental staging. Start and stop times in same db table.

Discussion on moving ZFA to GO like model; possibility of implementing VAO import (so that XAO can just clone this VAO chunk when they also clone the rest of ZFA)

• Aaron and Jeff:
  • Discussion on setting up modular ontology model and specifics of importing model species-specific information (like devo stage)