Difference between revisions of "WBConfCall 2016.09.01-Agenda and Minutes"
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= Agenda = | = Agenda = | ||
| − | == Standing | + | == Standing items == |
| − | === Use | + | === Updates from AGR working groups === |
| − | === Disease / Phenotype === | + | * Use-case |
| + | * Disease / Phenotype | ||
| + | * Orthology | ||
| + | * Tools | ||
| + | === Help Desk tickets requiring attention === | ||
| + | * User asking about use of RESTful API; https://github.com/WormBase/website/issues/5069 | ||
| + | |||
| + | = Minutes = | ||
| + | |||
| + | == Todd == | ||
| + | * Was in a car accident; will need to minimize work load and screen time (emergencies only for now) | ||
| + | * Should we put the next build (WS256) on hold? Probably not. OICR won't need to start the working on WS256 for ~4 weeks | ||
| + | * Sibyl could possibly attempt to stage WS256, Juancarlos could provide assistance | ||
| + | |||
| + | == Working Groups == | ||
| + | |||
| + | === Use Cases === | ||
| + | * Have had 2 meetings so far | ||
| + | * Having some difficulty in defining the scope of user stories/use cases for the AGR portal | ||
| + | * Also, not clear if there is a development group we should be immediately handing off use-cases to | ||
| + | * We've done a cross-comparison of data presented on gene pages at each MOD | ||
| + | * Started building wire-frame diagrams for the process of querying AGR on a gene and arriving at a gene page | ||
| + | * We have identified several input/output pairs of data; input is what query is based on/seeded with; output is what data a user is attempting to retrieve | ||
| + | * We are individually working on defining many user stories starting with different input data types | ||
| + | * We will sort and prioritize the list of user stories and start developing use-cases for the top user stories | ||
| + | * It may be best use of time to first outline what is on a gene page and how users would query for genes | ||
| + | |||
| + | === Disease/Phenotype === | ||
| + | * 2 meetings so far | ||
| + | * What objects do people curate to? | ||
| + | * What are the ontologies and controlled vocabularies that are used? | ||
| + | * There's a mixed bag; group will work on defining standards that everyone can use | ||
| + | * The Disease Ontology (DO) was decided to be a central ontology to use; some funding for DO in question | ||
| + | * Mouse group has been working heavily with DO and OMIM | ||
| + | * OMIM have their own curators and annotation style, not quite ready for receiving input from outside databases/groups | ||
| + | * Discussing curation of NOTs; when a disease model might be expected, capture when it doesn't turn out to be | ||
| + | |||
=== Orthology === | === Orthology === | ||
| − | + | * Only 3 members (PIs) up until this week; others joined this week | |
| + | * Currently working on defining canonical protein sets | ||
| + | * Would use UniProt reference proteome; up to date for some organisms (yeast, fly, worm), not all (not mouse, zebrafish, rat) | ||
| + | * UniProt working on getting up to date | ||
| + | * Canonical zebrafish protein set defined by Ensembl/Havana(sp?) | ||
| + | * Why doesn't UniProt have an up to date protein set for zebrafish? | ||
| + | * Mouse: money/effort spent on curating protein sets for mouse at EBI; not clear how mouse databases (MGI) use the Ensembl data | ||
| + | * Rat canonical protein set also not clearly defined in UniProt | ||
| + | * Will learn more in upcoming meeting | ||
| − | = | + | == Caltech will discuss single-cell RNA profiling == |
| + | * What do we think about mapping sequence reads from these data sets? | ||
| + | * We will try to incoporate all available data; some back log to work through | ||
| + | * Each paper has their own pipelines/processes for analysis of data; how do we want to capture/accommodate this data? | ||
Latest revision as of 17:29, 1 September 2016
Contents
Agenda
Standing items
Updates from AGR working groups
- Use-case
- Disease / Phenotype
- Orthology
- Tools
Help Desk tickets requiring attention
- User asking about use of RESTful API; https://github.com/WormBase/website/issues/5069
Minutes
Todd
- Was in a car accident; will need to minimize work load and screen time (emergencies only for now)
- Should we put the next build (WS256) on hold? Probably not. OICR won't need to start the working on WS256 for ~4 weeks
- Sibyl could possibly attempt to stage WS256, Juancarlos could provide assistance
Working Groups
Use Cases
- Have had 2 meetings so far
- Having some difficulty in defining the scope of user stories/use cases for the AGR portal
- Also, not clear if there is a development group we should be immediately handing off use-cases to
- We've done a cross-comparison of data presented on gene pages at each MOD
- Started building wire-frame diagrams for the process of querying AGR on a gene and arriving at a gene page
- We have identified several input/output pairs of data; input is what query is based on/seeded with; output is what data a user is attempting to retrieve
- We are individually working on defining many user stories starting with different input data types
- We will sort and prioritize the list of user stories and start developing use-cases for the top user stories
- It may be best use of time to first outline what is on a gene page and how users would query for genes
Disease/Phenotype
- 2 meetings so far
- What objects do people curate to?
- What are the ontologies and controlled vocabularies that are used?
- There's a mixed bag; group will work on defining standards that everyone can use
- The Disease Ontology (DO) was decided to be a central ontology to use; some funding for DO in question
- Mouse group has been working heavily with DO and OMIM
- OMIM have their own curators and annotation style, not quite ready for receiving input from outside databases/groups
- Discussing curation of NOTs; when a disease model might be expected, capture when it doesn't turn out to be
Orthology
- Only 3 members (PIs) up until this week; others joined this week
- Currently working on defining canonical protein sets
- Would use UniProt reference proteome; up to date for some organisms (yeast, fly, worm), not all (not mouse, zebrafish, rat)
- UniProt working on getting up to date
- Canonical zebrafish protein set defined by Ensembl/Havana(sp?)
- Why doesn't UniProt have an up to date protein set for zebrafish?
- Mouse: money/effort spent on curating protein sets for mouse at EBI; not clear how mouse databases (MGI) use the Ensembl data
- Rat canonical protein set also not clearly defined in UniProt
- Will learn more in upcoming meeting
Caltech will discuss single-cell RNA profiling
- What do we think about mapping sequence reads from these data sets?
- We will try to incoporate all available data; some back log to work through
- Each paper has their own pipelines/processes for analysis of data; how do we want to capture/accommodate this data?
