Difference between revisions of "WormBase-Caltech Weekly Calls"
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* 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 | * 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) | * 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.) |
Revision as of 16:32, 15 April 2021
Previous Years
2021 Meetings
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.
- Propose to move possible_pseudonym (192) and Other_animal (37) to remarks. Those tags are not currently used for curation.
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
- Pharos: https://pharos.nih.gov/
- could we contribute?
- Visualization, tools, etc.
- Automated person descriptions?
- Automated descriptions for proteins, ion channels, druggable targets, etc.?
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 \°\;
- 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.)