Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2017|2017 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2018|2018 Meetings]]
  
GoToMeeting link: https://www.gotomeet.me/wormbase1
+
[[WormBase-Caltech_Weekly_Calls_2019|2019 Meetings]]
  
 +
[[WormBase-Caltech_Weekly_Calls_2020|2020 Meetings]]
  
= 2018 Meetings =
+
= 2021 Meetings =
  
[[WormBase-Caltech_Weekly_Calls_January_2018|January]]
+
[[WormBase-Caltech_Weekly_Calls_January_2021|January]]
  
[[WormBase-Caltech_Weekly_Calls_February_2018|February]]
+
[[WormBase-Caltech_Weekly_Calls_February_2021|February]]
  
[[WormBase-Caltech_Weekly_Calls_March_2018|March]]
+
[[WormBase-Caltech_Weekly_Calls_March_2021|March]]
  
[[WormBase-Caltech_Weekly_Calls_April_2018|April]]
 
  
[[WormBase-Caltech_Weekly_Calls_May_2018|May]]
+
== April 1, 2021 ==
  
[[WormBase-Caltech_Weekly_Calls_June_2018|June]]
+
=== Antibodies ===
 +
* Alignment of the antibody class to Alliance:
 +
** Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
 +
*** Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both  in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
 +
*** Possible pseudonym was used when  a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
 +
** Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.
  
[[WormBase-Caltech_Weekly_Calls_July_2018|July]]
+
All changes proposed above were approved by the group
  
 +
=== textpress-dev clean up ===
 +
* Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
 +
* is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
 +
* Direct access may be possible via Caltech VPN
 +
* Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines
  
== August 2, 2018 ==
+
=== Braun servers ===
 +
* 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
 +
* Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know
  
=== AFP ===
+
=== Citace upload ===
 +
* Next Friday, April 9th, by end of the day
 +
* Wen will contact Paul Davis for the frozen WS280 models file
  
* The AFP pipeline is currently emailing authors from karen's e-mail address
 
* Use same e-mail account Chris is using for phenotype community curation requests or create a new account for AFP (gmail)
 
* Can use outreach@wormbase.org for consistency
 
* May use the PMID in the subject line so e-mails will not be all in the same thread
 
* Todd and Chris have email credentials
 
** Chris will send to Valerio, Juancarlos, Daniela, and Kimberly
 
* Let Valerio and Juancarlos know what pipelines use AFP before they modify
 
* Do curators still want to receive emails when authors flag their data type?
 
** We will leave the alert emails as is for now
 
  
 +
== April 8, 2021 ==
  
== August 9, 2018 ==
+
=== Braun server outage ===
 +
* Raymond fixed; now Spica, wobr and wobr2 are back up
  
=== AFP ===
+
=== Textpresso API ===
* Mei Zhen, SAB member suggested that we include disease models in the AFP form.
+
* Was down yesterday affecting WormiCloud; Michael has fixed
* The AFP group will work with Ranjana to incorporate it. Ranjana will prepare a mock by next week.
+
* Valerio will learn how to manage the API for the future
* We will then decide about using the existing afp_humdis tables or creating new ones.
 
  
=== Tazendra ===
+
=== Grant opportunities ===
 +
* Possibilities to apply for supplements
 +
* May 15th deadline
 +
* Druggable genome project
 +
** Pharos: https://pharos.nih.gov/
 +
** could we contribute?
 +
* Visualization, tools, etc.
 +
* Automated person descriptions?
 +
* Automated descriptions for proteins, ion channels, druggable targets, etc.?
  
* Shall we move tazendra.caltech.edu to the cloud? Either WormBase cloud or Caltech cloud?
+
=== New WS280 ONTOLOGY FTP directory ===
 +
* Changes requested here: https://github.com/WormBase/website/issues/7900
 +
* Here's the FTP URL: ftp://ftp.wormbase.org/pub/wormbase/releases/WS280/ONTOLOGY/
 +
* Known issues (Chris will report):
 +
** Ontology files are provided as ".gaf" in addition to ".obo"; we need to remove the ".gaf" OBO files
 +
** Some files are duplicated and/or have inappropriate file extensions
  
 +
=== Odd characters in Postgres ===
 +
* Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
 +
* Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
 +
* We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
 +
* Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters
  
  
== August 16, 2018 ==
+
== April 15, 2021 ==
  
=== Tazendra ===
+
=== Special characters in Postgres/OA ===
* Moving to cloud? To avoid local hardware issues?
+
* Juancarlos working on/proposing a plan to store UTF-8 characters in Postgres and the OA which would then get converted, at dumping, to HTML entities (e.g. α) for the ACE files
* Need to discuss with Juancarlos and Paul S.
+
* There is still a bit of cleanup needed to fix or remove special characters (not necessarily UTF-8) that apparently got munged upon copy/pasting into the OA in the past
* Need to consider logistics; put all of Tazendra functionality on cloud? Keep some things local?
+
* Note: copy/paste from a PDF often works fine, but sometimes does not work as expected so manual intervention would be needed (e.g. entering Greek characters by hand in UTF-8 format)
** Postgres in cloud; forms local? Paper pipeline?
+
* Would copy/pasting from HTML be better than PDF?
** Will consult with Textpresso
+
* For Person curation it would be good to be able to faithfully store and display appropriate foreign characters (e.g. Chinese characters, Danish characters, etc.)
 +
* Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
 +
** Juancarlos will modify script to take a data type code as an argument on the command line and return all Postgres tables (and their respective PGIDs) that have special characters, e.g.
 +
*** $ ./get_summary_characters.pl exp
 +
*** $ ./get_summary_characters.pl int
 +
*** $ ./get_summary_characters.pl grg
 +
** or could pass just the datatype + field (postgres table). e.g.
 +
*** $ ./get_summary_characters.pl pic_description
 +
** Juancarlos will email everyone once it's ready.  It's ready, email sent.  Script is at /home/postgres/work/pgpopulation/oa_general/20210411_unicode_html/get_summary_characters.pl  Symlink this to your directory and run it from there, it will create files in the directory you are at when running it.
 +
* Action items:
 +
** Juancarlos will update the "get_summary_characters.pl" script as described above
 +
** Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
 +
** Need to perform bulk (automated) replacement of existing HTML entities into corresponding UTF-8 characters
 +
** Curators will need to work with Juancarlos for each OA to modify the dumper
 +
** Juancarlos will write (or append to existing) Postgres/OA dumping scripts to:
 +
*** 1) Convert UTF-8 characters to HTML entities in ACE files
 +
*** 2) Convert special quote and hyphen characters into simple versions that don't need special handling
  
=== ICBO 2018 recap ===
+
=== CeNGEN pictures ===
* POTATO workshop (Phenotype Ontologies Traversing All The Organisms)
+
* Model change went in to accommodate images from the CeNGEN project
** Will work towards generating standardized logical definitions using Dead Simple OWL Design Patterns (DOSDP)
+
* Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
*** <Quality> and inheres_in some <Entity> (and has_modifier some <Mod>)
+
* Raymond and Daniela will work with data producers to acquire images when ready
*** Exercise: Reconciling logical definitions for apparently equivalent phenotype terms across ontologies (e.g. MP vs. HP)
 
** Can use Protege to edit the OWL ontology and ROBOT for automating generation of many terms and logical definitions in parallel
 
** Will try to align WPO to UPheno as best as we can; will depend (at least in part) heavily on alignment with Uberon for anatomy
 
** Some Uberon alignment challenges: e.g. Fruit fly "tibia" and human "tibia"; human "tibia" parent is "bone" but fly "tibia" is not a bone
 
** Will participate in Phenotype Ontology Developer's call, every 2 weeks on Tuesdays (9am Pacific, 12pm East coast, 5pm UK)
 
*** Next meeting September 4, 2018
 
** Crash course in Protege, ROBOT, Ontology Development Kit, using GitHub to help develop OWL ontologies
 
** PATO needs work
 
** Questions that arose:
 
*** What should the scope of an ontology term be? Context? Life stage? Conditions? Treatment?
 
*** Being weary of ontology term count explosion; what's the right balance?
 
*** When defining phenotype terms, should the cause be included or only the observation? Maybe causes as a subclass (and assuming the observation includes assessment of cause)
 
** Some distinction between human phenotype terms and model organism terms: phenotype of individual vs. population
 
* Xenbase is trying to develop a phenotype ontology (spoke with Troy Pell, developer)
 
** Asked about WPO and how we curate
 
* Lots of plant talks
 
* Many talks on performing quality checks on ontology development and ontology re-use
 
* Domain Informational Vocabulary Extraction (DIVE) tool
 
** Entity recognition/extraction
 
** Working with two plant journals
 
** Tries to identify co-occurrence patterns of words
 
** Web interface and curation tool
 
* Semantic similarity tools and evaluation of them
 
  
=== WormBase Phenotype Ontology working group ===
+
=== Supplement opportunities ===
* Chris will send around Doodle poll
+
* Money available for software development to "harden" existing software
* Goal is to discuss creation of logical definitions and alignment of phenotypes for Alliance
+
* Might be possible to make Eduardo's single cell analysis tools more sustainable
 +
* Could make WormiCloud adapted to Alliance?
 +
* Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)
  
 
+
=== Student project for Textpresso ===
== August 23, 2018 ==
+
* Create tool to allow user to submit text and return a list of similar papers
 
+
* Use cases:
=== Alliance tables ===
+
** curator wants an alert to find papers similar to what they've curated
* Filtering/sorting priorities
+
** look for potential reviewers of a paper based on similar text content
* Open question about which tables on the Alliance website should be prioritized for acquiring sorting and filtering functionality
 
 
 
=== Worm Phenotype Ontology working group ===
 
* Gary S., Karen, Kimberly, and Chris have responded to [https://doodle.com/poll/xzkxet8sb57enver#table Doodle poll]
 
* Looks like 12pm Pacific (3pm Eastern) on Thursdays is the time that works for everyone
 
** May start late on days when WB CIT meeting goes past 12pm Pacific
 
** May want to start a bit past 12pm to allow west coasters to get lunch, etc.?
 
* Goals:
 
** Work on logical definitions for WPO terms
 
** Consider any restructuring of WPO that would facilitate ontology alignment with other MODs and UPheno
 
** Could we eventually create a phenotype annotation tool (and term requester) that allows modular expressions of a phenotype observation to lookup existing terms or create new terms with logical definitions based on those modular elements?
 
 
 
=== Alliance anatomy ===
 
* Data quartermasters and expression working group are looking to get updated anatomy-Uberon mappings
 
* How frequent are data updates at the Alliance? Seems to be every ~2 months
 
* Anatomy-Uberon mappings will affect phenotype ontology alignments
 
 
 
=== Automated Gene Descriptions ===
 
*Ranjana and Valerio working to finish the new pipeline for automated descriptions for WB, will aim to finish them for the next upload, WS269.
 
* Working on one of the last data types--tissue expression; will use the anatomy ontology to perform logical trimming for the annotation set of cell/anatomy types (for each gene) including neurons (as opposed to using a file for neuronal term groupings taken from Oliver Hobert paper in the old pipeline)
 
* Currently playing around with thresholds to see how the sentences look, will feedback any ontology related issues to Raymond
 
* Working on incorporating feedback from users for information-poor genes (defined as genes with no human orthology and no GO annotations). Will include other types of information suggested by Users such as human ortholog function and protein domains, etc.
 
* When no other data is available, will include expression cluster data.  Users have complained that they don't find this data useful as it's non-specific and from large scale studies, so will give it the lowest priority for inclusion.
 
*Suggestion to exclude the writing and storing of the thousands of automated descriptions to the Postgres database; there is really no advantage in them being in Postgres. 
 
* At the time of generation of the automated descriptions the related .ace files can also be generated; though will need to include the 6000+ manual descriptions that live in Postgres.  So will need to rethink this part a bit, though skipping Postgres will reduce the number of manual steps in the pipleline and Postgres will have less data that needs to be uploaded and downloaded from future cloud storage.
 

Latest revision as of 19:34, 15 April 2021

Previous Years

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2011 Meetings

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2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

January

February

March


April 1, 2021

Antibodies

  • Alignment of the antibody class to Alliance:
    • Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
      • Other animal is sometimes used for older annotations, e.g. authors say that the antibodies were raised both in rats and rabbits. Standard practice would create 2 records, one for the rat antibody and one for the rabbit.
      • Possible pseudonym was used when a curator was not able to unambiguously assign a previous antibody to a record. (we have a Other name -synonym- tag to capture unambiguous ones). When moving to remarks we can keep a controlled vocabulary for easy future parsing, e.g. “possible_pseudonym:”
    • Antigen field: currently separated into Protein, peptide, and other_antigen (e.g.: homogenate of early C.elegans embryos, sperm). Propose to use just one antigen field to capture antigen info.

All changes proposed above were approved by the group

textpress-dev clean up

  • Michael has asked curators to assess what they have on textpresso-dev as it will not be around forever :-(
  • is it okay to transfer data and files we want to keep to tazendra? and then to our own individual machines?
  • Direct access may be possible via Caltech VPN
  • Do we want to move content to AWS? May be complicated; it is still easy and cheap to maintain local file systems/machines

Braun servers

  • 3 servers stored in Braun server room; is there a new contact person for accessing these servers?
  • Mike Miranda replacement just getting settled; Paul will find out who is managing the server room and let Raymond know

Citace upload

  • Next Friday, April 9th, by end of the day
  • Wen will contact Paul Davis for the frozen WS280 models file


April 8, 2021

Braun server outage

  • Raymond fixed; now Spica, wobr and wobr2 are back up

Textpresso API

  • Was down yesterday affecting WormiCloud; Michael has fixed
  • Valerio will learn how to manage the API for the future

Grant opportunities

  • Possibilities to apply for supplements
  • May 15th deadline
  • Druggable genome project
  • Visualization, tools, etc.
  • Automated person descriptions?
  • Automated descriptions for proteins, ion channels, druggable targets, etc.?

New WS280 ONTOLOGY FTP directory

Odd characters in Postgres

  • Daniela and Juancarlos discovered some errors with respect to special characters pasted into the OA
  • Daniela would like to automatically pull in micropublication text (e.g. figure captions) into Postgres
  • We would need an automated way to convert special characters, like degree symbols ° into html unicode \&deg\;
  • Juancarlos and Valerio will look into possibly switching from a Perl module to a Python module to handle special characters


April 15, 2021

Special characters in Postgres/OA

  • Juancarlos working on/proposing a plan to store UTF-8 characters in Postgres and the OA which would then get converted, at dumping, to HTML entities (e.g. α) for the ACE files
  • There is still a bit of cleanup needed to fix or remove special characters (not necessarily UTF-8) that apparently got munged upon copy/pasting into the OA in the past
  • Note: copy/paste from a PDF often works fine, but sometimes does not work as expected so manual intervention would be needed (e.g. entering Greek characters by hand in UTF-8 format)
  • Would copy/pasting from HTML be better than PDF?
  • For Person curation it would be good to be able to faithfully store and display appropriate foreign characters (e.g. Chinese characters, Danish characters, etc.)
  • Mangolassi script called "get_summary_characters.pl" located here: /home/postgres/work/pgpopulation/grg_generegulation/20200618_summary_characters
    • Juancarlos will modify script to take a data type code as an argument on the command line and return all Postgres tables (and their respective PGIDs) that have special characters, e.g.
      • $ ./get_summary_characters.pl exp
      • $ ./get_summary_characters.pl int
      • $ ./get_summary_characters.pl grg
    • or could pass just the datatype + field (postgres table). e.g.
      • $ ./get_summary_characters.pl pic_description
    • Juancarlos will email everyone once it's ready. It's ready, email sent. Script is at /home/postgres/work/pgpopulation/oa_general/20210411_unicode_html/get_summary_characters.pl Symlink this to your directory and run it from there, it will create files in the directory you are at when running it.
  • Action items:
    • Juancarlos will update the "get_summary_characters.pl" script as described above
    • Curators should use the "get_summary_characters.pl" to look for (potentially) bad characters in their OAs/Postgres tables
    • Need to perform bulk (automated) replacement of existing HTML entities into corresponding UTF-8 characters
    • Curators will need to work with Juancarlos for each OA to modify the dumper
    • Juancarlos will write (or append to existing) Postgres/OA dumping scripts to:
      • 1) Convert UTF-8 characters to HTML entities in ACE files
      • 2) Convert special quote and hyphen characters into simple versions that don't need special handling

CeNGEN pictures

  • Model change went in to accommodate images from the CeNGEN project
  • Want gene page images for CeNGEN data; have the specifications for such images been worked out? Maybe not yet
  • Raymond and Daniela will work with data producers to acquire images when ready

Supplement opportunities

  • Money available for software development to "harden" existing software
  • Might be possible to make Eduardo's single cell analysis tools more sustainable
  • Could make WormiCloud adapted to Alliance?
  • Put Noctua on more stable production footing? (GO cannot apply as they are in final year of existing grant)

Student project for Textpresso

  • Create tool to allow user to submit text and return a list of similar papers
  • Use cases:
    • curator wants an alert to find papers similar to what they've curated
    • look for potential reviewers of a paper based on similar text content