Third Face to Face Meeting

Agenda

1. Compare and align perspectives within the team.
2. Use case development and documentation.
   • Compilation and organization of existing use cases into a standard format, with clear path to collaboration and publication. Existing use cases can be grouped into:
     • Those described with Campanulaceae in the project proposal:
       1. Clarifying and comparing different definitions of a single taxon
       2. Identifying species within a dataset belonging to a particular clade definition
       3. Identifying where a clade definition resolves on a taxonomy
       4. Referring to clades that have yet to be formally defined (also applied to "dark taxa" in bacteria and viruses)
     • Raised in the second F2F meeting:
       1. Comparing alternate concepts of a taxon (same as above)
       2. Tracking the history of alternate concepts of a taxon (same as above, but with a temporal component)
       3. Something to do with data integration
       4. Upcoming challenges in communicating poorly-understood taxa
       5. Chrome/Firefox widget for phyloreference resolution
       6. Trait-oriented research projects
       7. Build a Protege plugin for phyloreferencing in Protege
   • Discussion of new use cases proposed since the second F2F meeting (October 2017)
     • List current use cases here
3. Review project aims and goals and discuss future goals
   1. Curation Workflow
      • Plan for version 1.0: required features
      • Development timeline
   2. Curation Tool
      • Plan for version 1.0: required features
      • Development timeline
   3. Ad-hoc experiments with Open Tree API
      • Plans for integrating into the Curation Tool
   4. Phyloreferencing Specification and Ontology
      • Plan for release of complete, working draft
   5. Integration with PhyloRegnum
      • Regnum-to-Phyloreference conversion software
      • Phyloreference-to-Regnum conversion software
   6. Phyloreferencing demonstration website
      • Needs to meet two project aims:
        • A proof-of-concept application for utility and correctness of phyloreferences
        • A proof-of-concept application for navigating large-scale data resources
      • Overall development goal for May to September
      • What does this tool look like? What features will it need? How can we best demonstrate phyloreferencing?
4. Clarify what phyloreferencing can/cannot do. Theoretical and practical considerations for phyloreferencing.
5. Wild ideas
   • Use natural language to query a phylogeny.
   • Phylogeny-aware data query.
   • A continuously updated display of clade contents, as in Hibbett et al, 2005
6. Minor topics for one-on-one discussions:
   • (GV + HL) Merging vs squashing in Git records
7. Plan for Advisory Board meeting, April 23, 2018.
8. Upcoming meetings and travels
   • TDWG2018. Aug 25-Sep 02, New Zealand. Symposium status: 12 applications & 5 abstracts submitted.
   • idigbio Berkeley meeting. Dates: Jun 04-06. Abstract deadline: Apr 30.
9. Add other items for discussion here or insert where relevant above

Schedule

• Wednesday, March 21
  • Morning: Compare and align perspectives within the team.
  • Morning: What can/cannot phyloreferencing do? What should we focus on for use cases?
  • Afternoon: Use case development and documentation.
• Thursday, March 22
  • Morning: Use case development and documentation.
  • Afternoon: Review project aims and goals and discuss future goals
• Friday, March 23
  • Morning: Review project aims and goals and discuss future goals
  • Afternoon: Wild ideas

Emergent tasks

(I'm checking off these tasks as I move them into Github projects and issues -- that does not mean that they have been completed! -- GGV)

High level goals

• What is the average time taken to create a phyloreference? What are the drivers of that time? (Start with imprecise per-hour basis so we have some idea) --> phyloref/curation-tool/projects/4
• Create and publish an ontology of phyloreferences in a timely manner
  • Curation Tool needs to be complete enough for curating (TOP) --> phyloref/curation-tool/projects/1
    • Start curating in earnest (AS SOON AS POSSIBLE)
  • Curation Tool needs to reason so that phyloreferences can be tested. (SECOND) --> phyloref/curation-tool/projects/2
  • Ontology is generated automatically from PHYX files. (THIRD) --> phyloref/curation-workflow/projects/3
• Develop user stories and use cases. (AT LEAST 3 PRESENTABLE USER STORIES/USE CASES -> BY APRIL 20)
• Prepare for the Advisory Board meeting. (BY APRIL 23)
• Write the ontology of phyloreferences paper. (BY SEPTEMBER)
• Next F2F meeting in October (+/- 1 month) (FALL)

For Gaurav

• Rewrite TDWG abstract TONIGHT, send for review and apply for travel grant.
• Phyloref ontology to remain at phyloref/phyloref-ontology, so file issues there.
• Move all scratch ontology terms into the issue tracker so we can move them into the Ontology as needed. --> phyloref/phyloref-ontology/labels/new term, phyloref/curation-workflow#20
• Update and review the phyloreferencing specification.
• Issues with the Curation Tool:
  • Make selected phyloreferences brighter --> phyloref/curation-tool#12
  • Make a button next to the phyloref label so it goes directly to the node in the phylogeny --> phyloref/curation-tool#13
  • Name parsing service for scientific names → name parsing, iPlant TNRS --> phyloref/curation-tool#14, phyloref/curation-tool#15
  • Make components of scientific names editable. --> phyloref/curation-tool#16
  • Parse content of the clade definition and try to read it into the specifiers --> phyloref/curation-tool#18
  • Add support for muting specifiers? --> phyloref/curation-tool#19
  • Add support for identifying specimens with scientific names --> phyloref/curation-tool#20
  • Add support for extracting name even when the specifier starts with “Type: “ — indicating that this is the type species? --> phyloref/curation-tool#21
  • Change the background of selected elements instead of changing the foreground --> phyloref/curation-tool#12
    • You are reducing contrast when you change the color away from black
    • Not everybody has as strong and keen eyes as I do — exaggerate the contrast by my standards to help other people see what’s going on!
  • Retain the full text of the specifier in the specifier information --> phyloref/curation-tool#17
  • Give the user an immediate understanding of what the machine knows --> phyloref/curation-tool#22, phyloref/curation-tool#23
  • The taxonomic unit screen is the place to show the detailed breakdown of what we see from each taxonomic unit --> phyloref/curation-tool#22
    • We do have a lot of real-estate to play with: maybe go back to merging the different types into the same thing?
  • We need some kind of visual prompt to indicate that the name has been parsed (or that we couldn’t clearly differentiate genus/species etc.) --> phyloref/curation-tool#14
  • We need to add support for specimens that are identified purely from genetic data — bacteria --> phyloref/curation-tool#20
  • Add support for cases what the taxonomic unit is identified by a sequence ID, even when it isn’t the sequence ID (we already cover that with external references to GenBank) --> phyloref/curation-tool#20
  • Note that a specimen HTTP URI --> phyloref/curation-tool#20
  • Add support for adding the collection code as a separate field (maybe Darwin Core Triplet it a little bit) --> phyloref/curation-tool#16
  • Allow curators to make a note that you couldn’t match the specifier against the original phylogeny? --> phyloref/curation-tool#24
  • Add an option to the reasoner to ignore unmatched specifiers --> phyloref/curation-tool#19
    • Otherwise, we need to dig into the paper and pull out all possible information, including species name etc.
  • Add an option to the reasoner to OPTIONALLY ignore specifiers --> phyloref/jphyloref#5
    • It’s an unnecessary specifier!
  • Add assertions that a reviewer that checked this and found it acceptable. phyloref/curation-tool#26
    • Approved-by: … (ORCID)
    • Curator notes --> phyloref/curation-tool#24
  • Make it possible to edit the labels --> phyloref/curation-tool#27
  • Color code phyloreferences --> phyloref/curation-tool#25
  • New phyloreference → show me where this is on a tree --> phyloref/curation-tool#23,
  • Add a button to say “I’m done!” with the Phyloreference --> phyloref/curation-tool#25
    • If they are subsequently modified, they should go back into “incomplete” until completed.
    • It’s clearly not validated.
      • Incomplete → Unvalidated → Validated
  • Add “Validate/Verify/Test” button to phyloreferences --> phyloref/curation-tool#25
  • Rename the Curation Workflow to an Ontology of Phyloreferences. --> phyloref/curation-workflow#19
  • Upload to Github. --> phyloref/curation-tool#29
    • Do it earlier rather than later.
  • What do we want to call these files? --> phyloref/curation-workflow#21
    • Test case
    • Study
    • Phyloreference … ?
      • Not “ontology file” — although it kind of is!
      • Phyloreference Exchange format (PHYX, pronounced phix)
      • Gets deposited to Github rather than someone’s personal drive
  • JSON-LD representation of phylogeny will allow labels to be included within the phylogeny --> phyloref/curation-workflow#22

For Guanyang

• Start collecting phylogenies in preparation of curation
• User stories and use case development

For Hilmar

For Nico

• Obtain permission to curate certain phyloreferences
• Modify PhyloRegnum to support data depositories (via data DOIs) and to encourage the upload of Newick, NeXML and image files.