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Data Jamboree 2/Notes

User interface

User interface demonstration

DATE? SUNDAY MEETING OR DO THESE NOTES ALSO APPLY TO MEETING WITH INDIVIDUALS IN PAIRS ON MONDAY/TUESDAY/WED?

MGI batch query demo

User interface strategy

Feedback and Suggestions on proposed Phenoscape UI

Taxon Concepts subgroup meeting (Monday, Sept. 29, 2008)

(Present: Peter Midford, Paula Mabee, Todd Vision, Wasila Dahdul, Hilmar Lapp, John Lundberg, Suzi Lewis, Judy Blake)

Synonym scanner is working well but will never be perfect because CoF doesn’t list every synonym in existence (because they may not detect every use in literature, or maybe deemed a name not worthy of addition as synonym)

TJP (TV?): Have we checked requested taxa not in CoF against UBio? - that would provide an LSID that could provide a dbxref to anchor the taxon

Addition of synonyms not in TTO: currently Peter must add by hand.

Need to track - Association between synonym, person who requested and publication? - Not being tracked right now.

JGL: We don’t want to give this to CoF because these synonyms are picked up in morphological or phylogenetic studies. These names that appear and we flag as synonyms to valid names in CoF are not names coming out of taxonomic research; these are mistakes: OCR, typographical mistakes of author, or author mistakes of species in wrong genus.

Seems we should track all of this in database?

We want: - author year of the reference (right now it’s in comments) - want in a searchable context - does CoF have a database of publications?

PM: ed publication information (DOI, SCSI) -CoF has an internal reference - We also need to record the full citation ourselves (name, year, unpublished dissertation…)

Peter: dbxref from CoF can be added to TTO; OBO ontologies are structured to hold dbxrefs, whole references in any structured way.

synonym reference - how should it be handled?

SL: synonym xref can be a person (initials)

to summarize: full text ref would be in db; ontology would have a pointer to that

Peter: need interface to the db; won’t be visible to obo-edit - make the dbxref a url link to URI

TV: We need a universal place to resolve that URL

PM: synonym types necessary? misspellings; narrow etc…

Peter: Hoping we can scan stuff in from CoF

JGL: see ANSP collection search: type in a type specimen name and it pulls in the CoF ref need CoF identifier; CASspec?

PM: who should do this?

JGL: why can’t curator do this?

PM: too much time; can be done in bulk

Peter: synonym types: - current vocab is exact, related, broader, narrower - all synonyms currently are related (the weakest relation). - we will want misspelling to be even weaker than related; - distinguish between published synonomy vs, curator made decision

HL: weighing how trustworthy the evidence vs. designation of weak/strong; to HL, misspelling is a strong exact synonym not weak

PM: are misspelings the only exact synonyms?

TV: not critical to have the types of synonyms; just use related

all in agreement (misspellings will be taken as exact, other taxonomic synonyms use related).

Hilmar’s notes

There are taxonomic names that are found in publications and are absent from TTO.

Evidence for synonym to current name assignment needs to be recorded.

Action items

Notes from Data Curation Sessions

Sylvan Lake Lodge Meeting Room - September 29, 2008 (Monday)

Wasila & Paula’s notes

Comparative phenotypes: discussion of relative size, shape characters: Problem: Descriptors comparing size, shape among taxa within a pub cannot be extended to taxa outside the study (e.g., Rick’s size of bone example with three character states: large (0), small (1), extremely small (2)) How to do this with ontologies? Judy pointed out that there is a (dynamic line)in annotation, between the depth of a structured vocabulary and free text. I.e. where do you stop using an ontology and begin using free text? Data specific to study should be free-text.

Judy Blake intially suggested simply annotating our complex anatomical characters to “shape”. This indexing first pass is useful for users to be able to aggregate the data (vs. full curation). Through further discussion, we agree that annotating to a more granular level, i.e. “shape: width” would be better and more informative. The weakness of the current PATO comes in here, in that there need to be more nodes between shape and all the terminal nodes (the descriptors such as “narrow” “broad” etc.). This might allow more depth than just “shape:width”.

We need to index our comparative systematic studies at a level that is useful for the field. It is like a library, “binning” index to multiple things.

John’s idea for recording size comparison within a study: Use shape: width and ALSO apply an internal grading system for these characters such that the least/smallest value is given 1.

Eric’s example of incomplete/complete scute series:

Judy: important to separate tasks of 1) anatomy ontology development and 2) annotation of publications

Mark submitted TAO request on Weberian vertebra - relationships that don’t hold for all taxa

Wasila: batching vs. one term request: ok to submit related terms in one request

Suzi: suggested having a small PATO workshop with ichthyologists, like anatomy workshop

curators understand details of system

JB: put 2-3 people together to do anatomical subtree: send out invite to ontology development

Judy’s observation notes

Wrap-up discussion with curators

October 1, 2008 (Wed morning)

Wasila + Paula’s notes

Paula: suggestions for improving curation process?

Paula: Problem: Currently we are not curating of entities that are always present (e.g. “maxilla” present in all Teleostei). Problem is that users may search for distribution of a character and may find variability in very restricted taxon (genus) but have no information as to the condition in the larger group (teleost fishes). Need to add these conserved characters. Two approaches - either fine for us - need input from Jim regarding database feasibility.

Action items:

Curation consistency experiment: Review of Results

Five curators (Engeman, Grande, Hilton, Mayden, Sabaj) participated in the consistency experiment on September 30, 2008 (Wed.). The results of the experiment are discussed in more detail here.

Hilmar’s notes on discussion of experiment with curators and advisors

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