WormBase-Caltech Weekly Calls
Contents
- 1 Previous Years
- 2 2022 Meetings
- 2.1 September 14th, 2023
- 2.2 September 7th, 2023
- 2.3 August 31st, 2023
- 2.4 August 24th, 2023
- 2.5 August 3rd, 2023
- 2.6 July 20th, 2023
- 2.7 Place for teaching material
- 2.8 Making Web pages for uPub papers
- 2.9 WormBook and GSA
- 2.10 Connectome
- 2.11 Release announcements
- 2.12 July 13th, 2023
- 2.13 July 6th, 2023
- 2.14 June 8th, 2023
- 2.15 June 1st, 2023
- 2.16 May 25th, 2023
- 2.17 May 11th, 2023
- 2.18 May 4th, 2023
- 2.19 April 27th, 2023
- 2.20 March 23rd, 2023
- 2.21 March 16th, 2023
- 2.22 March 9th, 2023
- 3 Feb 23rd, 2023
- 4 Feb 9th, 2023
- 5 January 26th, 2023
- 6 January 5th, 2023
- 7 December 8th, 2022
- 8 November 17th, 2022
- 9 November 3rd, 2022
- 10 October 27, 2022
- 11 October 6th, 2022
- 12 Aug 25th, 2022
- 13 Aug 18th, 2022
- 14 Aug 11th, 2022
- 15 July 28th, 2022
- 16 July 14th, 2022
- 17 June 30, 2022
- 18 June 23, 2022
- 19 May 26, 2022
- 20 May 12, 2022
Previous Years
2022 Meetings
September 14th, 2023
Switching over to the new textpresso-labs cloud system
For the next upload instructions-September 26th
All the curators will dump their files on the old Tazendra system. They will then copy the files on the dockerized system - acedb@caltech-curation.textpressolab.com
/usr/caltech_curation_files/Data_for_citace/Data_from_<insertcuratorname>/
/usr/caltech_curation_files/Data_for_CitaceMinus/ /usr/caltech_curation_files/Data_for_Ontology/
Wen does the build on that.
You must test your ace files on the CitaceMinus mirror.
Switch to the dockerized system right after the upload - on October 2nd
September 7th, 2023
Paper Issue
- WBPaper00062523 republished as WBPaper00063966 (Daniel)
- WBPaper00062523 is a biorxiv paper entered about a month before the reviewed publication came in
- There's no data attached to the biorxiv paper that I can see, so is it okay to make it invalid?
- Confirm that we're not bringing in preprints from biorxiv (this is also what the Alliance lit group agreed) - do we need to re-visit this decision?
- WBPaper00062523 made invalid in postgres (not merged into WBPaper00063966 since these are separate publications)
citace upload
- Status update for test file generation and upload
- Confirm:
- Where to deposit the .ace file
- How will the files get there?
- Review file archive/backup policy - where and for how long?
- Dumping script updates SOP
- Modify script in github
August 31st, 2023
Alliance Migration: Review flagged data types
- Discuss future of the different data types and flagging methods in context of transferring data to the Alliance infrastructure
- Initially thought we were planning to transfer everything we have currently at Caltech
- But are there data types that we don't need to transfer, and if so, what are the implications for:
- Alliance data storage - any limitations?
- Storing and accessing existing Caltech legacy data
- If we don't transfer legacy data, but a flagging pipeline still runs, do we stop the flagging pipeline? Keep the flagging pipeline but don't transfer any new data to the Alliance?
- I can make a table like the one below for all the data types, if this would be helpful. (Kimberly)
Data Type in Curation Status Form | Data Type Definition (same for each flagging method?) | Flagging method(s) in curation status form | Current usage - which flagging methods are currently used for curation | Alliance migration - which flagging method(s) data to transfer to the Alliance | Curators | Alliance curation and data modeling status |
---|---|---|---|---|---|---|
Antibody | For example: This flags papers that describe..... | NNC, SVM, String Match, cfp, afp, oa, curation status | Daniela, Wen, Xiaodong |
Next citace upload using dockerized tazendra 2-Oct-2023
- Documentation for SOP
- Decided at meeting that we'll do the transfer on Sept 14 after discussing at the meeting.
- Everyone please test your usual curation to make sure everything works before we switch over, or we'll switch over and your stuff won't work until we fix it.
Minimum requirements for variation and strain ace files
Strain : "WBStrainID" - Required and auto-generated on submission (not entered by curator)
Strain Public_name "ABC1" - Required
Reference WBPaperId - Required
Genotype "optional, if provided" - Optional
Remark "Free text" Curator_confirmed "Your WBPersonID" - Optional
Species "Caenorhabditis elegans" - Required
Live - Required and auto-generated on submission (not entered by curator)
Variation : WBVarID - Required and auto-generated on submission (not entered by curator)
Variation Public_name "abc1" - Required
Reference WBPaperId - Required
Gene "WBGeneID" - Optional
Strain "optional, if provided" - Optional
Remark "Optional free text" Curator_confirmed "Your WBPersonID" - Optional
Species "Caenorhabditis elegans" - Required
Live - Required and auto-generated on submission (not entered by curator)
- Full class models:
?Variation class ?Variation Evidence #Evidence Name Public_name UNIQUE ?Variation_name XREF Public_name_for Other_name ?Variation_name XREF Other_name_for #Evidence Rearrangement ?Rearrangement XREF Variation // some alleles are really rearrangements HGVSg UNIQUE Text #Evidence Sequence_details SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Allele Flanking_sequences UNIQUE Text UNIQUE Text Mapping_target UNIQUE ?Sequence Source_location UNIQUE Int UNIQUE ?Sequence UNIQUE Int UNIQUE Int UNIQUE #Evidence //source data, <WSversion> ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks) CGH_deleted_probes UNIQUE Text UNIQUE Text CGH_flanking_probes UNIQUE Text UNIQUE Text Type_of_mutation Substitution UNIQUE Text UNIQUE Text #Evidence // wild type and mutant sequence Insertion UNIQUE Text #Evidence Deletion UNIQUE Text #Evidence Tandem_duplication #Evidence PCR_product ?PCR_product XREF Variation SeqStatus UNIQUE Not_sequenced //[2006-02-17 ar2] to differentiate between mutations which have been sequenced and those which have not. Sequenced Pending_curation Deletion_verification Text #Evidence //[14-Mar-06 ar2] Mark Edgely of KO_alleles has developed test to confirm deletion (mt3) Variation_type Engineered_allele //construct model addition Allele SNP // replaces the old 'Status Text' part of ?Locus model Confirmed_SNP Predicted_SNP RFLP Reference_strain_digest Text Text Text // storing site, enzyme, and band size Polymorphic_strain_digest Text Text Text Transposon_insertion ?Transposon_family XREF In_variation Natural_variant Origin Species UNIQUE ?Species Strain ?Strain XREF Variation #Evidence Component_of_genotype ?Genotype XREF Variation Laboratory ?Laboratory Author ?Author // use Person when known, else use Author Person ?Person // Analysis ?Analysis Corresponding_transgene UNIQUE ?Transgene XREF Corresponding_variation Production_method CRISPR_Cas9 Homologous_recombination //Homologous_recombination MosSci MosDEL NHEJ //Non-homologous DNA end-joining, imprecise DNA repair TALENs ZFNNHEJ_repair //Zinc-finger nuclease ZFNHR_repair Expr_pattern ?Expr_pattern XREF Variation #Evidence DB_info Database ?Database ?Database_field UNIQUE ?Text //to link out to KO pages ar2 02-DEC-05 KO_consortium_allele // North American knockout consortium NBP_allele // Japanese knockout consortium NemaGENETAG_consortium_allele //NemaGENETAG consortium allele - Nektarios et al Detection_method Text Positive_clone ?Clone XREF Positive_variation #Evidence Nature_of_variation UNIQUE Polymorphic Synthetic History Merged_into UNIQUE ?Variation XREF Acquires_merge Acquires_merge ?Variation XREF Merged_into Split_from UNIQUE ?Variation XREF Split_into Split_into ?Variation XREF Split_from Status UNIQUE Live #Evidence Suppressed #Evidence Dead #Evidence Linked_to ?Variation XREF Linked_to // for being able to specify paired substitutions which are part of the same allele Affects Gene ?Gene XREF Allele #Molecular_change //#Molecular_change mh6 define precise changes [060217 ar2] Predicted_CDS ?CDS XREF Variation #Molecular_change Transcript ?Transcript XREF Variation #Molecular_change Pseudogene ?Pseudogene XREF Variation #Molecular_change Feature ?Feature XREF Associated_with_variation Interactor ?Interaction XREF Variation_interactor Possibly_affects ?Gene XREF Possibly_affected_by #Evidence Isolation Date DateType Mutagen UNIQUE Text #Evidence Forward_genetics Text #Evidence // Capture the basis of the experiment that isolated Reverse_genetics Text #Evidence // the allele. [040206 krb] Transposon_excision ?Transposon_family Derived_from_variation ?Variation XREF Derivative Derivative ?Variation XREF Derived_from_variation Derived_from_construct ?Construct XREF Engineered_variation Genetics Gene_class ?Gene_class XREF Variation Mating_efficiency Male UNIQUE ME0_Mating_not_successful #Evidence ME1_Mating_rarely_successful #Evidence ME2_Mating_usually_successful #Evidence ME3_Mating_always_successful #Evidence Hermaphrodite UNIQUE HME0_Mating_not_successful #Evidence HME1_Mating_rarely_successful #Evidence HME2_Mating_usually_successful #Evidence HME3_Mating_always_successful #Evidence Map ?Map XREF Variation #Map_position Interpolated_map_position UNIQUE ?Map UNIQUE Float Mapping_data 2_point ?2_point_data Multi_point ?Multi_pt_data Pos_neg_data ?Pos_neg_data // above three are for mapping on its own behalf In_2_point ?2_point_data In_multi_point ?Multi_pt_data In_pos_neg_data ?Pos_neg_data // these are for when the locus is mapped Marked_rearrangement ?Rearrangement XREF By_variation Description Phenotype ?Phenotype XREF Variation #Phenotype_info Phenotype_remark ?Text #Evidence Phenotype_not_observed ?Phenotype XREF Not_in_Variation #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes Disease_info Models_disease ?DO_term XREF Disease_model_variation Modifies_disease ?DO_term XREF Disease_modifier_variation //New tag Models_disease_in_annotation ?Disease_model_annotation XREF Variation //New tag Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_variation //New tag Modifies_disease_asserted_variation ?Disease_model_annotation XREF Asserted_variation // request for WS287 Reference ?Paper XREF Allele Remark ?Text #Evidence Method UNIQUE ?Method Supporting_data Movie ?Movie XREF Variation #Evidence //Carol [060421 ar2] ?Variation_name Other_name_for ?Variation XREF Other_name // main reason for this class Public_name_for ?Variation XREF Public_name // the main name for a gene // hash to contain detailed changes caused by mutations [2006-02-17 ar2] #Molecular_change VEP_consequence Text // proposed addition as well as mapping to the WB tags. VEP_impact Text #Evidence SIFT Float Text #Evidence PolyPhen Float Text #Evidence HGVSc Text #Evidence HGVSp Text #Evidence cDNA_position Text #Evidence CDS_position Text #Evidence Protein_position Text #Evidence Intron_number Text #Evidence Exon_number Text #Evidence Codon_change Text #Evidence Amino_acid_change Text #Evidence ?Strain class ?Strain Evidence #Evidence Status UNIQUE Live #Evidence Dead #Evidence Genotype UNIQUE Text Public_name UNIQUE ?Text Other_name ?Text #Evidence Contains Gene ?Gene XREF Strain Variation ?Variation XREF Strain Rearrangement ?Rearrangement XREF Strain Clone ?Clone XREF In_strain Transgene ?Transgene XREF Strain Disease_info Models_disease ?DO_term XREF Disease_model_strain Modifies_disease ?DO_term XREF Disease_modifier_strain //New tag Models_disease_in_annotation ?Disease_model_annotation XREF Strain //New tag Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_strain //New tag Database ?Database ?Database_field ?Text Properties Inbreeding_state UNIQUE Selfed Text Isofemale Text Multifemale Text Inbred Text Outcrossed UNIQUE Text Mutagen Text Strain_history Text Date_first_frozen UNIQUE DateType CGC_received DateType Phenotype ?Phenotype XREF Strain #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_Strain #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes Location ?Laboratory #Lab_Location Made_by ?Person //updated from ?text Contact ?Person Remark ?Text #Evidence Reference ?Paper XREF Strain Species UNIQUE ?Species // added by krb [021021] NCBITaxonomyID UNIQUE Int // Allows for finer grade attachment of NCBItaxon IDs Wild_isolate // to identify wild isolates - since genotype is free text Isolation GPS UNIQUE Float UNIQUE Float #Position_confidence // Latitude +/-DD.DDDDD Longitude +/-DD.DDDDD Elevation UNIQUE Float #Position_confidence // Elevation above sea level. Place UNIQUE ?Text Landscape UNIQUE Urban_garden Forest Wild_grassland Agricultural_land Oasis Rural_garden Botanical_garden_zoo Wet_shrubland Dry_shrubland Substrate UNIQUE ?Text // e.g. snail, soil, apple, rotting fruit Associated_organisms ?Text Life_stage ?Life_stage Log_size_of_population UNIQUE Float Sampled_by Text // the person who found the worms Isolated_by ?Person // the person who isolated the worms from the sample Date UNIQUE DateType Picture ?Picture
August 24th, 2023
- Using name server as a backdoor for curation
- Minting WBIDs for Tier3 and 4 species
August 3rd, 2023
Caltech
- Reminder to do research integrity training
- Not everyone at WormBase got the email - Paul S. can double-check if this was based on job titles or something else
Genetics Database Update Paper
- Is there enough material for a WB update?
- Explanation of transition to the Alliance
- Start by creating a table of data types in WB vs Alliance
- New WB data, e.g. single cell data
- Explanation of transition to the Alliance
- If so, who's turn is it to write it?
July 20th, 2023
Remaining debrief from IWM
- PIs wanting to undergraduates to do more in terms of curation and training
- check into training support with NSF community outreach grants
Motivating the community
- Chris's trophys a huge hit - people wanted pictures and were motivated
- $250 uPub voucher useful
- Paul's sense of swag is off, staff have great ideas
- WB blog supports images - can post pictures of trophy winners
Place for teaching material
want to have a public location to for people to access webinars and slides etc. ex. XenBase
Paul suggests we use an Alliance Forum to post these, will also motivate alliance members to do the same>
Chris suggests the Alliance User Forum
Todd suggests Google drive is good, but many problems with things getting muddled, e.g, by inconsistent naming = things get lost and hard to find
If we use google drive, need to have some management
Do we want a place for the community to share things with the community
Alliance User Support Group should be tapped for help here, and we can reach out to GSA to see what they do to organize community teaching docs.
Raymond - CMS system is designed for this, but we would need to set that up == Wen is interested
Todd- need to identify what type of material would we be putting up. Slide shows? - maybe use a ready built CMS that is good with side-shows, will also need to have maintenance over time.
Maybe the lowest hanging fruit is just Maintaining an Index page for these, then it doesn't matter where the material really exits
Start with generic index page at Alliance, with brief metadata - can we store it in CaltechData = Karen and Wen will talk to the library
Making Web pages for uPub papers
Immediate problem - make a splash page for paper not found at WB.
something more general - ask Alliance for splash page
gene paper links is going to be more complicated
WormBook and GSA
Genetics thinking that WormBook is not that active, but possibly they are missing out on activity since community uses WormBook.org as index to find articles.
Dainel has been adding Genetics WormBook chapters to WormBook.org, so they should be available there and findable.
Connectome
Raymond fixed the link-outs to these sites, not updated on the site yet
Todd- hotfix will be run that should fix all of that
Release announcements
Not automated, Caltech needs to synchronize things, Raymond and Wen will be added to Slack release channel.
July 13th, 2023
Update/Discussion on WormBase -> Alliance paper pipeline migration
- Alliance data model for entity/topic tagging
- Alliance Tags for Papers Ontology
- ECO requests
- Bibliographic data - Alliance will be the source of truth for all references in PubMed (except legacy author data); WB will be the source of truth for all other paper, e.g. meeting abstracts
- Entity tags
- Species
- Modeling evidence
- 'Manually_connected' plus 'Curator_confirmed' - Alliance doesn't yet have people, so we will store 'WBPerson' in a created_by field
- 'Inferred_automatically' text string (from ACKnowledge pipeline)
- No explicit evidence in postgres, but notes on what we did, e.g. scripts and string matching
- Modeling evidence
- Genes
- Modeling evidence
- Species
- Topic tags
- Will port over the WB topic and map to an ATP ontology term
- Will not populate species (we don't know this definitively at WB)
- Each flagging 'method' will be a unique combination of: source, source details, MOD, and creator
- For example, author, ACKnowledge, WB, WBPerson625
- For example, author, Fast Track Your Paper, FB, Norbert Perrimon
- Some data types, e.g. antibody, are modeled as topics and entities; we will only populate topic unless we also have a specific curie to populate an entity value
- New topic tags: antibody data
- Existing validation will come from manual curator entries in curation status form and from OA values and from author ACKnowledge submissions
- Each validation is tracked separately; no manual validation will overwrite any other manual validation
- Manual entries will validate AI entries (more specific entries can validate less specific entries)
- Modeling and porting over curation status pre-canned comments
- SVM positive, curation negative
- Validated right by curator, but not curatable for WB (will be a new workflow ATP tag)
- WB may not have always been consistent here, so we may want to think about clean up after migration
- C. elegans as heterologous expression system
- GO curation (will not port over; we can get this information from a GAF, if need be)
- BioGrid and BioGrid/GO - keep?
- Curation negative, no strain name given in paper
- Toxicology - create an ATP value?
- Host-pathogen virulence - create an ATP value?
- SVM positive, curation negative
July 6th, 2023
June 8th, 2023
- Update on WormBase -> Alliance paper pipeline migration
- Newly added WB papers for retraction notices and corrections
June 1st, 2023
- Raymond: We need to prepare some slides to introduce our tools at IWM. It would be better to drop them to the google doc folder for IWM.
- From Tazendra to Amazon Cloud server: Valerio finished the backup setting and now restoring data on the cloud server. Now testing Wen's script and the full build will be tested after IWM
- Textpresso will be modified and prepared for ABC in Alliance. This will be discussed again after IWM.
May 25th, 2023
- Waterston data
- Noticed that Bob's list had 69 dead genes and that the graphs were displayed on the dead gene page
e.g. WBGene00009022 https://wormbase.org/species/c_elegans/gene/WBGene00009022#0g1--10
- Asked Paulo to map the dead genes to the live ones and display on the live gene page.
- While doing this Paulo noticed that 55 genes had values for both dead and live genes, and the values are quite different.
https://wormbase.org/species/c_elegans/gene/WBGene00007084#0g1--10
- Notify Bob, can ditch dead genes
May 11th, 2023
- Waterston data update
- Generated a file with the correct mappings
- Renamed Canopus the image files on Canopus
- Generated a -D file for Citace Minus
- Send the .ace file to stavros
- Contact Paulo and Todd
- Tested on spica, all good
- Patch the file for WS289. What needs to be done?
- Next upload
- Falls right after the IWM and around the 4th of July holiday
- Do we want to do a trial upload with our new system beforehand?
- We will upload the files on spica as we normally do but will also test the new system as much as we can
- Will do upload on July 11th
- IWM
- Finalize swag
- Generic WB swag pens and frisbee (agreed blue with white logo): https://docs.google.com/document/d/1v8bCoL2Qy9hNQmJ57YOccg8HkmKXclulugfnYwGU7lM/edit
- Community curation swag: https://www.crownawards.com/search?q=FIRDBW&lang=default
- Trophies with custom logos: https://www.crownawards.com/Custom_Logo_Trophies?q=FIRDBW
- Booth
- Ordered 2 chairs, a long desk, 1 electric outlet. Sarah D, Stavros will bring additional chairs
- Carpeting. ok without
- Finalize swag
- Backup for new dockerized system
- Restic software -command line program that provides encrypted backup. Files compressed and store by md5sum
- want to avoid the encryption if we can
- Can include folders
- symlinks to the scripts -> will back up the links but not the files, which will be backed up with git
- Include/exclude list for files and folders
- Documentation will be provided in a readme file in github
- Backup files can be stored in aws S3
- Person wormbase_comments in acedb vs internal comments in postgres, but neither on WBPerson pages on website.
- No one recalls why they're in acedb, email sent to wormbase@caltech with questions for Cecilia. There are ~14k wormbase_comments
May 4th, 2023
- Bug with molecule OA
- JSON parse failed error -> fixed
- Juancarlos will look into this
- Alliance postgres migration
- Chris started working on this
April 27th, 2023
- 445 image files provided by Bob Waterston contain the wrong WBGene name, e.g. egl-1_WBGene00001186_embryo_lineage.jpg (egl-1 is WBGene00001170)
- noticed while doing spot check in discussing Eyleen J. O'Rourke data
- Paulo programmatically went through the files, the graphs are unaffected, the images are.
- Option 1: ask Juancarlos to rename the wrong image files, based on gene public name. Prepare a -D file for CitaceMinus and re-upload a .ace file for the wrong objects.
- Option 2: ask Bob to send again the original files with the right name.
- Regardless, notify Bob
March 23rd, 2023
- Some updates on Neural Networks development (postponed)
March 16th, 2023
- Getting data from acedb to load postgres. (e.g. Variation) Do we still need this ? Automated scripts seemed to break a lot, while running them manually always worked.
March 9th, 2023
- [migration to the cloud]
- The generic.cgi, we need to know who uses these:
- tempVariationObo: this brings in variations into the OA that are in WB but not in the OA. Note this is a different functionality compared to the Name server. We need this. Used by Ranjana, ??
- CG: Yes, I need this
- UpdateVariationObo--can't get to this now on Tazendra
- AddToVariationObo--can't get to this now on Tazendra
- TempStrainObo --brings in strains into the OA that are in WB, seems to be the counterpart of the tempVariationObo for strains
- CG: I need this
- AddTempObjectObo--used to add data to the database, used by AddToVariationObo and AddToStrainObo
- PapIdToWBPaper
- CG: I need this
- When people added things by mistake they would sometimes remove them from the flatfile, does anyone still do that ? -- Chris and Ranjana don't, Karen or Daniela might
- Does the public need access to this, or should we move this to a private / protected URL ? -- Nick/micropub probably needs this
- tempVariationObo: this brings in variations into the OA that are in WB but not in the OA. Note this is a different functionality compared to the Name server. We need this. Used by Ranjana, ??
- WSVariation and nightly geneace variation file
- Overlapping but WSVariation has a lot more variation-related info, e.g. phenotype and phenotype_not_observed
- Confirming that we still need both
- There's also WpaXref and WpaXrefBackwards and ListPmids and ConvertPaperIdentifiers
- The only thing is that it writes to flatfiles so when cronjobs update variation/strains from nameserver or WS, it also loads from the flat files. The location of the flatfiles isn't final yet, but it's dockerized. People used to manually edit that when they wanted to remove them from the list, do people still want to manually edit those flatfiles ?
- ContinentPIs
- Valerio has set up ssh access into textpressolab.com
- There's 3 cases for using acedb:
- your local use for testing stuff
- spica replacement for Wen
- extract things automatically for tazendra/postgres. Do we need this ?
- The generic.cgi, we need to know who uses these:
- Some updates on Neural Networks development
Feb 23rd, 2023
New paper folder organization may affect downstream pipelines
- Antibody string-matching pipeline was affected by recent changes in paper folder structure
- The pipeline started processing old papers, does this affect also papers processed for NN?
- http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?action=listCurationStatisticsPapersPage&select_datatypesource=caltech&select_curator=two12028&listDatatype=antibody&method=str%20pos%20nval&checkbox_cfp=on&checkbox_afp=on&checkbox_str=on&checkbox_nnc=on&checkbox_svm=on
Feb 9th, 2023
IWM 2023 booth cost
- From Mary Anne this morning: "I had the cost wrong, it would be $750 for you at cost. Sorry, I had been looking at the wrong line item."
January 26th, 2023
Alliance issues
- monitoring API usage?
- We have Google Analytics but since Patrick Kalita left, no one has been monitoring it
- Paul: we need for now a simple way of tracking number of users. Chris: seems reinventing the wheel to write something from scratch. tracking API calls would be useful for our funders.
- Olin said you can track UI events (e.g. page clicks) and API access (including programmatic access) but we are not currently. Chris will see how much work is involved in this. We need someone with Google Analytics experience.
- Would be good to put a call out to all people at Alliance asking who has experience with Google Analytics.
- Simplemine: reverse proxy hosted at alliancegenome.org. If it is dockerized we can do it, otherwise not. Eventually dockerize Simplemine and move it to Alliance servers.
- Olin concerned about security over CGI technology.
- We will talk about this (implementation and security concerns) at the developer call
- Embedding alliance tools or processes into MODs.
- The API is there but is not in all MOD interest to write code to pull the data out.
- iFrame is not very flexible on how you display data (e.g. narrow, little flexibility in configuration).
- Could set up widgets as we did for the GO ribbon. Still requires MOD implementation of code base.
- Paul: eventually MOD sites will be retired. Chris: One concern from Christian (ZFIN): clicking on a zebrafish gene name will open up an alliance page, could it link to ZFIN gene page or provide users with an option?
- Maybe opening up an Alliance widget at the MOD preferably happens in a separate window (e.g. pop-up window, new browser window/tab; as opposed to in the same page/tab).
Alliance All Hands
- Not all the curators are going to be there. Focus on PI discussion and development teams?
January 5th, 2023
- Chris will help to create a reverse proxy for the Alliance SimpleMine. It will function like WormBase SimpleMine. People will need to visit the Alliance before going to tazendra. It will prevent users from seeing the tazendra URL and create more traffic for the Alliance
- Alliance SimpleMine with XenBase data is ready but needs XenBase feedback before it goes public. It is based on Alliance 5.4.0 release, so it can be released when Alliance 5.4.0 goes public in late Jan or mid-Feb.
- Karen will visit Pasadena 1/13-15
December 8th, 2022
Data Type Flagging Pipelines and Alliance Infrastructure
- We currently run the neural network algorithms at Caltech
- What will we need to do to transition this to run on Alliance infrastructure?
- Can we start to run the neural networks on a more frequent basis, e.g. monthly? Could that be automated?
WB PDF Migration
- Daniel, Juancarlos, Kimberly continue some clean up of redundant files before moving things over to the Alliance
November 17th, 2022
- TEC_RED meeting. Meeting with Nikita Jahveri, Wouter Van de Berg (Gupta's lab). Participants, Valerio, Daniela, Kimberly, Magda, Stavros.
identified a large number of operons in C Briggsae. Baghwathi Gupta's lab. 4200 Briggsae genes identified with SL influencers. Want to contribute the information in WormBase.
- Used WS279 for the annotations
- they have excel documents with the location in the supplementary files
- Magda: are the tag sequences unique? Nikita: yes. If they bind to 2 ore more genes that have classified as paralogs
- Also identified isoforms (multiple transcripts tab in the spreadsheet)
- Steps forward: need to update the gene models and the operon models on WormBase.
- Can bring in data in different tracks.
- Need to update gene models based on this new evidence
- Nikita will send the data to Magda and Stavros (3 spreadsheets). Need to write out the categories.
- they did not produce the GFF file, all in excel sheets.
- Material used: mixed stage worm population
they have excel documents with the location
November 3rd, 2022
- Booth at IWM
- ACKnowledge will be showcased at the WB booth
- Will also advertise Alliance
October 27, 2022
October 6th, 2022
Mangolassi
- Mangolassi is down (network only?); Michael will be in the office in an hour
- Start a cronjob to check for network connections? Already set up (Raymond)
- Michael can log into his machine; Tazendra is OK (so, not network issue?)
- Michael fixed it by unplugging and reconnecting ethernet cable (network card issue)
GO meeting next week
- 7am - 11am PDT
- Zoom channel? Available on GO meeting agenda page:
Alliance Literature working group
- Subgroups; Ranjana interested in joining the search subgroup
- Can sign up on the lit group page
Persons
- Are there more use cases to collect?
- Some existing use cases:
- ACKnowledge attribution
- Community phenotype curators
- When do people need person IDs? When accessing/using some forms
- Content of earlier email
- When someone asks for a CGC Lab code, they must have a WBPerson ID. To fill out some tazendra forms, I think they need a WBPerson ID. To connect Persons to Laboratories for their WB lab page. To track who is a PI for which Lab. To connect to other Persons for Intellectual Lineage. Connect authors to Persons so Papers have a list of authors in publication order, each author linked to the Person (ZFIN has two lists, sorted for authors, separate for persons). Our users tell us they use the WB Person page for their cv.
- Use of Person Contact information: I think our use case for person information is mostly to have current emails for community outreach (ACKnowledge, community phenotype forms). It's been used in the past to send letters to PIs, so we could prioritize maintaining more information just for PIs. Some analysis is sometimes done by region / country, but this is rare. If anyone can think of other use cases for person data, please let us know. While we mostly only use the email addresses, Cecilia uses address / webpage / ORCID to connect authors to Persons, so having that data is important to make more connections.
- Knowing address and affiliation can help disambiguate similarly named persons/authors
- Questions about ethics of tracking information and person lineage?
- Not really a new issue; people present CVs on grants and other contexts
- Can be problematic to display people's email address and physical address, from a security perspective
- Email addresses: if someone has a strain/reagent not in a repository, can be helpful to connect to access materials
- We and others provide email addresses in publications
- We don't currently ask for permission to display the information (email, address, etc.); maybe we should?
- Should we have a survey to ask users' opinions about displaying this information? Is it worthwhile? Concerning?
- Should we provide a waiver that people agree their information will be in the public domain?
- Person form disclaimer: "Note: Phone and fax information won't show in your Person report for privacy reasons, but we are collecting the information in case we need to contact you. We keep old email, old institution, and old registered_lab data for history, please don't remove it when updating your information."
- Person form is available to public and displays personal information, e.g.: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person.cgi?action=Display&number=WBPerson51134
- Could someone scrape this information? Yes, person information is available from WB database dumps
- Could institute a login; we had wanted to keep the barrier to participate low
- Have 3 forms of privacy, where people can opt out of emails, hide their email address, or hide more information. If hidden it stays in Caltech postgres, and doesn't go to acedb.
- Going forward, the Alliance can implement better security for person information
Aug 25th, 2022
- Phosphoproteomic dataset
- WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application
Aug 18th, 2022
- Raymond reporting on meeting with Scott Emmons and neural connectivity data
Aug 11th, 2022
Secondary species information content.
- Gone through and counted number of objects in different data classes for all species
- https://docs.google.com/spreadsheets/d/1Q1FE7Miz0IJxultBtEq-VFoAcdz1UpxM3wfER4-qQGg/edit?usp=sharing
- Pristionchus: Talk to Ralf Sommer and see if wee can take some of the pristionchus.org data into WB -> Ranjana; Decision: after more discussion, decided to hold off on this as the plan is to focus on C. elegans for the grant. Perhaps in the future, we can seek finding and collaboration with the Pritionchus community (such as Sommer lab, etc).
- Brainstorm on how wee can utilize other species data -> may be a separate grant
- remanei (4 genome versions) and briggsae (3 genome versions) problem -> several versions of the genome. Same problem in parasite. Will need to address in the future. Want to have multiple sequence alignments so researchers can compare different versions.
- Address c elegans version assemblies in the grant. LoS from authors?
- Parasite has a new RNAseq analysis pipeline (not single cells yet)
July 28th, 2022
Global Core Biodata Resource application https://docs.google.com/document/d/1juJ4mm1evay32lNt3OOsbKL36RY4_3cW/edit?usp=sharing&ouid=106019143058337411488&rtpof=true&sd=true
July 14th, 2022
Reference and Person Evidence
- We need to know how best to move forward with ?Reference and ?Person evidence in the context of data exchange between WB and the Alliance
- Does A-team need to connect those WB Persons to be able to populate data in the Alliance curation db ?
- If so, can it wait until we have proper persons ?
- If not, when we have persons later will the data be reconnected to Person objects ?
- Where does data come from, which we call Person_evidence ? Some forms ? Direct emails ? Other sources ?
- For author curation/verification, what evidence do we want to use?
- Can we create Paper objects for the actual emails or other forms of communication (figure out details of when and what requirements), but keep Person_evidence for form submissions ?
- How much will it muddy things to create Paper objects for emails, e.g. how will it affect NLP downstream, do we need PDFs ?
- If we create personal communication References at Alliance only do we also want them as WBPapers, or will we just keep ?Person evidence at WB?
- Are we okay with conflating Person data and Paper data in Reference at the Alliance. That is, duplicating the same data as a Person and as a Reference.
How to look up balancers (Df / Dp) in WB (PWS/Ryan Baugh)
June 30, 2022
June 23, 2022
Helpdesk tickets
SOba in Alliance
GCBR application due 8th Aug
Prepare for grant; nice pics for metrics eg https://pharos.nih.gov
Should Alliance gene & allele model have Clone/Sequence name as an attribute?
May 26, 2022
WormBase user survey
May 12, 2022
Subcellular localization field
- WB has 2 separate free text fields to capture anatomical and subcellular localization statements but obviously the boundaries are fuzzy, see the example below where the statement belongs to both- there are many examples.
“miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.”
- Other MODs do not make such distinction.
- Daniela is asking the group advice to see if there is any objection in merging the 2 fields and slot the paragraph descriptions in the ExpressionExperimentStatement in LinkML.
- Decision: Keep just one field that will take care of both anatomical expression and subcellular localization
ExpressionExperimentStatement: is_a: EntityStatement description: >- Free-text describing some aspect(s) of a gene's expression, particularly nuanced information that is not readily captured in annotations. This statement's scope is limited to the associated ExpressionExperiment. notes: >- Inherits: statement_subject, statement_type, statement_text, references. slot_usage: statement_subject: range: ExpressionExperiment