|
|
| Line 35: |
Line 35: |
| | * ACKnowlegde pipeline help desk question: | | * ACKnowlegde pipeline help desk question: |
| | ** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM] | | ** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM] |
| − |
| |
| − |
| |
| − |
| |
| − | ==December 14, 2023==
| |
| − |
| |
| − | === C. elegans GPT ===
| |
| − | * Trained a small GPT model with C. elegans literature. Reporting some results.
| |
| − |
| |
| − | === Alliance Literature Migration ===
| |
| − | * [https://agr-jira.atlassian.net/browse/SCRUM-3556 WB tools connect to xref endpoint]
| |
| − | ** Requested Caltech curators to test on the [https://caltech-curation-dev.textpressolab.com/priv/cgi-bin/oa/ontology_annotator.cgi dev OA]
| |
| − | ** Would it help to set up a separate meeting to discuss together?
| |
| − |
| |
| − | * [https://agr-jira.atlassian.net/browse/SCRUM-3363 WB topics, how to process afp data]
| |
| − | ** Show Caltech curators a comparison between afp data in the Caltech curation status form vs the ABC. Implications for display and statistics.
| |
| − | ** Also, afp form had changes over its lifetime; ACKnowledge form has had different versions/releases with new fields
| |
| − | *** Example paper: WBPaper00046571 - afp flagged for geneint and newmutant in curation status form
| |
| − | *** Compare with ABC: https://stage-literature.alliancegenome.org/Biblio/?action=display&referenceCurie=AGRKB:101000000630958
| |
| − | ** Current data model at the ABC has negated as a Boolean (true/false).
| |
| − | *** We could add an additional value of 'null' to capture incomplete knowledge, i.e. unless we require authors (and curators) to always say Y/N for a given data type, we can't know for sure.
| |
| − | *** Maybe we just have to be explicit, for any future comparative analyses, that 'negative' validation by authors comes with a big caveats/limitations that we never required an explicit Y/N for every field and flagging by other methods, at least in some cases, suggests authors were not thorough
| |
| − |
| |
| − | ==December 07, 2023==
| |
| − |
| |
| − | === Alliance Literature Migration ===
| |
| − | ==== OA Paper Ontology switching to ABC ====
| |
| − | * Can we switch OA autocomplete / TermInfo / Validation to WBPapers in ABC ?
| |
| − | * Do we need to extract additional data from elsewhere. Or are there timing issues ?
| |
| − | * [https://agr-jira.atlassian.net/browse/SCRUM-3556 WB tools connect to xref endpoint]
| |
| − |
| |
| − | === Next citace upload ===
| |
| − | * This will be our first upload completely using the dockerized system.
| |
| − | * Tuesday, January 9th, for Caltech citace upload
| |
| − |
| |
| − | === TAGC ===
| |
| − | * Chris, Daniela, Karen, Kimberly, Nick, Wen attending
| |
| − | * Any outstanding registration issues?
| |
| − |
| |
| − |
| |
| − |
| |
| − | ==November 30, 2023==
| |
| − |
| |
| − | === WormBase Literature System Migration to Alliance ===
| |
| − | * Almost done with work for topic migration
| |
| − | ** Review ABC topic/entity table
| |
| − | ** Question about migration of OA 'curated' flag
| |
| − | *** Who/When curation was done in the OA is not stored in the curation status form
| |
| − | *** Do we need it? What do we want going forward when curation is performed at the Alliance?
| |
| − | * Objects curated and objects curated/paper fields in the curation status form
| |
| − | ** This raises the question of, at the Alliance, what information should be gathered from curation tools vs the ABC?
| |
| − | * Workflows and expectations for updating curated status for paper - data type
| |
| − | ** Instantaneous? Daily?
| |
| − |
| |
| − | === TAGC ===
| |
| − | * GSA membership renewal
| |
| − | * Meeting registration
| |
| − | * Accommodations
| |
| − |
| |
| − |
| |
| − | === Helpdesk ===
| |
| − |
| |
| − | please check recent tickets: #9379 and #9378
| |
| − |
| |
| − | FYI Stavros is on holiday until 4th of January. Please respond to the tickets that usually be responded by me. Thanks a million!
| |
| − |
| |
| − | Merry Christmas Everyone!
| |
| − |
| |
| − | ==November 9, 2023==
| |
| − | * TAGC
| |
| − | ** Who is attending - who is organizing what booth?
| |
| − | ** Can use passes, Exhibitors have
| |
| − | *** One full conference registration
| |
| − | *** Two exhibit hall-only registrations (additional booth personnel $50 each)
| |
| − | *** One guest pass
| |
| − | ** Announce on Alliance Forum?
| |
| − | *** Who to ask - David Shaw?
| |
| − |
| |
| − | * Literature system migration to Alliance
| |
| − | ** PDFs are now housed at the Alliance - any difficulties accessing?
| |
| − | ***Ranjana-Mostly works well for me whenever I've tried but haven't fully incorporated into my workflow
| |
| − | ***When will we be able to open a PDF (from the link) in the browser window which is really convenient instead of having to download it all the time? Did check my chrome browser settings and it is set to "Open PDFs in Chrome", so do I have to do something else or does something have to be done on the ABC side for the PDF to open in a browser window?
| |
| − | ** We are working on the UI for entity and topic addition
| |
| − | *** For entities that are not yet housed in the A team store, we will need to validate against WB
| |
| − | *** For new entities that are housed in the A team store, how will creating new ids work?
| |
| − | ** Textpresso for C. elegans
| |
| − | *** When to switch over to the Alliance instance?
| |
| − |
| |
| − | * Travel reimbursements status
| |
| − | ** Glasgow meeting
| |
| − | ** Other meetings
| |
| − |
| |
| − | * WS292 upload
| |
| − | ** Before or after the holidays?
| |
| − |
| |
| − | ==November 2, 2023==
| |
| − | * Expression Dataset Locator with scRNASeq datasets needs to show which version of WS the datasets are mapped to. A new column showing WS numbers will be good.
| |
| − | ** Alliance has no manpower to remap the scRNASeq from raw data.
| |
| − | * Church B167 will be taken back by BBE.
| |
| − |
| |
| − | ==October 12, 2023==
| |
| − | === Accessing FMS files at the Alliance ===
| |
| − | * FMS Swagger page: https://fms.alliancegenome.org/swagger-ui/index.html
| |
| − | ** Do not need credentials/authentication to run GET/read endpoints
| |
| − | ** Can use the Data File endpoints, provide data type name, like "HTPDATASET"
| |
| − | ** Can always see a list of all data types here: https://fms.alliancegenome.org/api/datatype/all
| |
| − | ** Can always see a list of all data subtypes here: https://fms.alliancegenome.org/api/datasubtype/all
| |
| − | * A-Team curation FMS page: https://curation.alliancegenome.org/#/fmspage
| |
| − | ** Make sure to update Release Version (e.g. 6.0.0 or 7.0.0)
| |
| − | ** Can filter "Data Type" column for data type of interest like "HTPDATASET"
| |
| − | ** Can see MD5 Sum of each file, download, etc.
| |
| − |
| |
| − | ==September 28th, 2023==
| |
| − |
| |
| − | ===Switching over to the new textpresso-labs cloud system===
| |
| − | * Juancarlos will flip the switch to the new dockerized system on Friday, Sep 29th
| |
| − |
| |
| − | === Research Integrity Course ===
| |
| − | * I (Chris G) still haven't completed this; is there a hard deadline?
| |
| − |
| |
| − | ==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 to the dockerized system - acedb@caltech-curation.textpressolab.com <br/>
| |
| − | **scp: scp -P 2022 <file> acedb@caltech-curation.textpressolab.com:/path/to/file/(-p is to specify port with ssh, -P is to specify port with scp. see below for rsync)
| |
| − | **/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 September 29th.
| |
| − |
| |
| − | == 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)
| |
| − |
| |
| − | {| class="wikitable"
| |
| − | !Data Type in Curation Status Form
| |
| − | ![https://docs.google.com/spreadsheets/d/1d3Y73x1BFiARkbxrvPPX2tCh5rFeBQRoBMHOcaXmijA/edit#gid=12026498 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
| |
| − | |-
| |
| − | |rowspan="1"|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:
| |
| − |
| |
| − | <pre>
| |
| − |
| |
| − | ?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
| |
| − |
| |
| − | </pre>
| |
| − |
| |
| − | == 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
| |
| − | * 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<br>
| |
| − | Paul suggests we use an Alliance Forum to post these, will also motivate alliance members to do the same><br>
| |
| − | Chris suggests the Alliance User Forum<br>
| |
| − | 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<br>
| |
| − | If we use google drive, need to have some management<br>
| |
| − | Do we want a place for the community to share things with the community<br>
| |
| − | 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. <br>
| |
| − | Raymond - CMS system is designed for this, but we would need to set that up == Wen is interested<br>
| |
| − | 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. <br>
| |
| − | Maybe the lowest hanging fruit is just Maintaining an Index page for these, then it doesn't matter where the material really exits<br>
| |
| − | 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 <br>
| |
| − | 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. <br>
| |
| − | 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<br>
| |
| − | 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 ===
| |
| − | * [https://docs.google.com/drawings/d/1dUt5PwBMBYf-x0ugzbJgMcsFWF-SvPU0bcYTo9YKI4s Alliance data model] for entity/topic tagging
| |
| − | * [https://alpha-curation.alliancegenome.org/#/ontology/atp Alliance Tags for Papers Ontology]
| |
| − | * [https://github.com/evidenceontology/evidenceontology/issues 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
| |
| − | ** Genes
| |
| − | *** Modeling evidence
| |
| − | * 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?
| |
| − |
| |
| − | == 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
| |
| − |
| |
| − | <pre>e.g. WBGene00009022
| |
| − | https://wormbase.org/species/c_elegans/gene/WBGene00009022#0g1--10 </pre>
| |
| − |
| |
| − | **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.
| |
| − |
| |
| − | <pre>https://wormbase.org/species/c_elegans/gene/WBGene00007084#0g1--10</pre>
| |
| − |
| |
| − | **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
| |
| − | * 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==
| |
| − | #[[https://docs.google.com/document/d/1aJ-TOd2xIxNV2VZG5T57brz3T82MMcgbyXWohVH27NU/edit?usp=sharing|Postgres 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
| |
| − | ##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 ?
| |
| − | #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
| |
