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Third Face to Face Meeting
Gaurav Vaidya edited this page Mar 27, 2018
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- Compare and align perspectives within the team.
- 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:
- Clarifying and comparing different definitions of a single taxon
- Identifying species within a dataset belonging to a particular clade definition
- Identifying where a clade definition resolves on a taxonomy
- 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:
- Comparing alternate concepts of a taxon (same as above)
- Tracking the history of alternate concepts of a taxon (same as above, but with a temporal component)
- Something to do with data integration
- Upcoming challenges in communicating poorly-understood taxa
- Chrome/Firefox widget for phyloreference resolution
- Trait-oriented research projects
- Build a Protege plugin for phyloreferencing in Protege
- Those described with Campanulaceae in the project proposal:
- Discussion of new use cases proposed since the second F2F meeting (October 2017)
- List current use cases here
- 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:
- Review project aims and goals and discuss future goals
- Curation Workflow
- Plan for version 1.0: required features
- Development timeline
- Curation Tool
- Plan for version 1.0: required features
- Development timeline
- Ad-hoc experiments with Open Tree API
- Plans for integrating into the Curation Tool
- Phyloreferencing Specification and Ontology
- Plan for release of complete, working draft
- Integration with PhyloRegnum
- Regnum-to-Phyloreference conversion software
- Phyloreference-to-Regnum conversion software
- 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?
- Needs to meet two project aims:
- Curation Workflow
- Clarify what phyloreferencing can/cannot do. Theoretical and practical considerations for phyloreferencing.
- 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
- Minor topics for one-on-one discussions:
- (GV + HL) Merging vs squashing in Git records
- Plan for Advisory Board meeting, April 23, 2018.
- 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.
- Add other items for discussion here or insert where relevant above
- 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
(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)
- 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
- Curation Tool needs to be complete enough for curating (TOP) --> phyloref/curation-tool/projects/1
- 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)
- 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
- Start collecting phylogenies in preparation of curation
- User stories and use case development
- 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.
Funded by the US National Science Foundation through collaborative grants DBI-1458484 and DBI-1458604. See Funding for details.