Topic pages

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back to' Caltech documentation
Other process related pages

Renaming this class

Pathways
Processes
Worm Processes
Process and Pathways Overview
Pathways and Processes
Biology
Worm Biology
Pathways and Biology

Goals of the process pages

  • Portal for larger biomedical community into C. elegans gene function.
  • Context for data that fits within a larger biological picture such as microarray results, and responses to chemical/drugs, i.e. orphaned data
  • On the fly update addendum to WormBook chapters
    • process pages will dissect the chapters and link them to entities in WormBase,
    • process pages will link summaries of processed with the most recent acedb data
  • Home for pathway views of data from Reactome, BioCyc, and Nemapath

Summary

A general summary of the process term. Can be extracted from WormBook if possible.

Genes

Genes related to the process with references.

  • Mined from GO
  • Mined from Phenotype
  • Assigned manually: coordinate with GO and Phenotype curators?

Cells / Anatomy

  • Mined from gene function?
  • Assigned manually from paper/reviews
  • Display should be embedded anatomy ontology window pointing to relevant cells/tissue objects.
  • Eventually, this should be the whole worm image or cell image (Neurobrowse where appropriate?)

Cell component

  • GO:CC associated with process with references.
  • Mined through gene GO assignments

GO biological processes

  • Embedded gene ontology window pointing to relevant GO biological process and genes.
  • Each process term will be manually mapped to a GO term, following the hierarchy of the GO ontology when useful

Phenotypes

  • Phenotypes from RNAi experiments, variations in major genes, discussed in reviews, with references.
  • Process terms will be associated with a phenotype through the GO2Phenotype mapping (curator validation will be needed)
  • For those phenotypes that are not associated through the GO2Phenotype mapping, a curator will do this manually, with feedback to GO and Phenotype curators for coordination of efforts.

Chemicals/small molecules

  • Drug/chemical/small molecule, CHEBI_ID, with references.

Genetic interactions

  • Manually associated
  • With the process with references.
  • Gene interaction networks (N-browse view?)

Microarray experiments

  • Expression clusters only (all microarray experiments should have these cluster views of the results)
  • link to SPELL page for microarray data

Related human disease

  • OMIM assignments based on process-associated genes, ranked by most evidence supported.

Subprocesses and pathways

  • List of processes based on WormBook and other reviews. Mined through GO hierarchy

Pathway/Reaction

Resources

  • WormBook (Viewed as WormBook chapter title and author (WBPerson/Author page))
  • WormAtlas (WormAtlas page(s) link, display page title)


Topic OAs

Process_term OA (prt_tables)

Fields are OA field name -- postgres table name -- .ace Tag --

TAB1

  • Curator -- prt_curator -- dropdown
  • WBbioprID -- prt_processid -- WBProcess -- (this field is required by the OA) auto-incremental based on new record dump as WBProcess:"WBbiopr:00000000" 8 digits
  • Process name -- prt_processname -- Public_name -- .ace dump as Public_name -- text
  • Summary -- prt_summary -- Summary -- big text
  • Other_name -- prt_othername -- Other_name -- big text, values will be pipe separated (note that looking for a process term in an OA WBProcess field will autocomplete first on WBbioprID, then process name, then this field. If you don't want this field to trigger autocomplete, let me know)
  • GO_term -- prt_goid -- GO_term -- multi-ontology for mapping process term to GO term, added 9/20
  • Specialisation_of -- prt_specialisationof -- Specialisation_of --multi-ontology for making heirarchical relationships of topics //added for WS244
  • Generalisation_of -- prt_generalisationof -- Generalisation_of --multi-ontology for making heirarchical relationships of topics //added for WS244
  • Remark -- prt_remark -- Remark -- big text
  • Paper -- prt_paper -- Reference -- multi-ontology autocomplete on WBPaperID

dumper at /home/postgres/work/citace_upload/process/ package is get_process_ace.pm script is use_process_package.pl

Model changes for WS243 - added Specialisation_of and Generalisation_of tags, removed Related_to For OA, Removed Related_process -- prt_relprocess -- data stored here /home/postgres/work/pgpopulation/prt_process_term/20140326_relprocess_backup] --kjy (talk) 20:05, 26 March 2014 (UTC)

--kjy 19:12, 13 June 2012 (UTC)

Topic Curation OA (pro_tables)

Fields are OA field name -- postgres table name -- .ace Tag --

TAB1

  • Curator -- pro_curator -- dropdown
  • WBPaper -- pro_paper -- Paper_evidence -- single ontology, autocomplete on WBPaperID; term info-WBProcess, Gene, GO terms (need to clear this w/ everyone)
  • Paper Primary Status -- pro_paperprimarystatus -- disabled OA field (not editable, read-only), not in model; displays whether paper is 'primary', 'non-primary' (research article vs. review, for example); updated nightly on cronjob
  • Topic Paper Status -- pro_topicpaperstatus -- Topic Paper Status dropdown; displays whether the paper is 'unchecked', 'relevant' or 'irrelevant'
  • Topic -- pro_process -- WBProcess -- single ontology (required field by OA) autocomplete (term and syn), store WBProcessID, term info, WBProcess ID, WBProcess, Summary, other_name, WBPaper
  • Gene -- pro_wbgene -- pro_paper #evidence-- Gene -- multi-ontology, autocomplete (public_name); term info-name, WBGeneID, WBProcess, WBPaper
  • Phenotype -- pro_phenotype -- Phenotype --pro_paper #evidence-- multi-ontology, autocomplete (name and syn); term info -description
  • Molecule -- pro_molecule -- Molecule -- pro_paper #evidence -- multi-ontology autocomplete (name and syn);term info-molecule ID, name, syn

TAB2

  • Anatomy_term -- pro_anatomy -- Anatomy_term -- pro_paper #evidence-- multi-ontology autocomplete on name; term info- name, WBbt ID, store ID
  • Life_stage -- pro_lifestage -- Life_stage -- pro_paper #evidence-- multi-ontology autocomplete on name; term info- name, store Life_stage ID
  • Taxon -- pro_taxon-- NCBITaxonomyID -- multi-ontology of NCBITaxonomy ID from pap_species_index, autocomplete on species name
  • Expression_cluster -- pro_exprcluster -- Expression_cluster -- pro_paper #evidence-- multi-ontology
  • Marker Construct -- ??? (CG added 12-12-2014; I don't know how this is used)

TAB3

  • Human_disease -- pro_humdisease -- text -- not in the model-- multi-ontology autocomplete on name and synonym text until file is ready for obo_ table
  • Topic Diagram -- pro_topicdiagram -- toggle -- not dumped, indicates that there is a relevant Topic diagram in the paper
  • Figuer Number -- pro_figurenumber -- text -- not dumped, indicates which figure in the paper contains a relevant Topic diagram
  • Picture -- pro_picture -- Picture -- pro_paper #evidence-- multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, expr. I remember we talked about this field, but not what we said, you'll be doing curation to pictures from here instead of picture curation adding processes ? -- J Yes --K
  • Movie -- pro_movie -- Movie -- pro_paper #evidence-- text -- until your file is ready for obo_ table
  • Pathway -- pro_pathwaydb -- dump the same way it is dumped for Interaction bigtext -- until file is ready for obo_ table, see http://wiki.wormbase.org/index.php/Gene_Interaction#Instructions_on_How_to_Use_the_New_OA for how to enter data.
  • Remark -- pro_remark --Remark--big text
  • (removed 9/20/13) GO_term -- pro_goid -- GO_term --pro_paper #evidence-- multi-ontology autocomplete (name and syn); term info -description

dumper at /home/postgres/work/citace_upload/process/ package is get_process_curation_ace.pm script is use_process_curation_package.pl

Paper Primary Status Cronjob

The cronjob to update the 'primary'/'non-primary' status of papers in the Topic OA is located on tazendra at: 

/home/postgres/work/pgpopulation/pro_process/cronjobs/populate_pro_paperprimarystatus.pl

This cronjob will run nightly at 4am or can be run manually from the directory above.

original OA

live on tazendra ran : /home/postgres/work/pgpopulation/pro_process/create_pro_tables.pl

TAB1

  • Curator-- curator -- -Move to top of TAB1-moved, dropdown, missing from specs, added here -- J
  • WBProcessID -- name -- auto-incremental based on new record dump as WBProcess : "WBbiopr:00000x" is this padding to 5 or 6 digits ? if we could do 8 or 10 that would be slightly easier -- J 8 to 10 total digits is fine--k k, using 8 -- J
  • Process_term -- processterm -- text
  • Summary -- summary -- big text
  • Other_name -- othername -- big text, values will be pipe separated
  • Related_process -- relprocess -- XREF to WBProcess -multi-ontology field, autocomplete on Process_term not on other_name ? -- J no, on process_term--k so it works ok ? -- J no, the processOA on mangolassi doesn't work.-k; works now! 1/13/12
  • WBProcess -- wbprocess -- ontology autocomplete on process_term same as the related_process ontology ? -- J, remove this table, it is not necessary --k, removed -- J
  • Remark -- remark -- big text
  • WBPaper -- paper --, -Move to bottom of TAB1, moved, multi-ontology autocomplete on WBPaperID; multiontology, term info-WBProcess, Gene, what ? from where ? This affects everyone that deals with WBPapers, which is everyone, so you'd have to clear it with everyone, unless I don't understand what you want. Temporarily added to sandbox. -- J, I have not heard from anyone, I'll ask at group meeting tomorrow -k, everyone has been asked -k changed live--J

TAB2

  • Expression_cluster -- exprcluster -- is multi-ontology now text until your file is ready for obo_ table -- J ok--k WS230ExprCluster.ace file from Wen deposited on tazendra/karen/processOA the ontology term info should include Expression_cluster (use for autocomplete), Description, Reference and Remark, there is no need to include Microarray_results or Algorithm. It's better if you put it in mangolassi, since we're doing development there. Will do when I'm back in the office, I don't have the password to mangolassi here. I scped to mangolassi, there's some problems, So the IDs are the Expression_cluster object names yes That's what it should store in postgres for dumping ?yes No synonyms, just autocomplete on the ID/object name ?correct The other tags you mentioned should just be data for Term Info display ? -- J yes Many tags are not explicitly meant to be included nor ignored : Anatomy_term, Based_on_WB_Release, Expr_pattern, Gene, Life_stage, Microarray_experiment, Regulated_by_gene, Regulated_by_molecule, Regulated_by_treatment. Correct, I did not want these information in the term info, no longer relevant- updating file through latest release AQL queries, See /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/err for lines referring to the tags. Also, are you going to wipe and repopulate or is this a static thing ?,I will be updating it after every citace upload, Let me know to give write permission to your account if you'll be rewriting to it. -- J, see comment after TODO, TODO when live, run /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/create_obo_tables.pl -- J DONE, No longer will use this script /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/populate_obo_exprcluster.pl -- J will repopulate file based on each new release as done with other OA ontologies; deposited expr_cluster.txt file on tazendra jolene/WS_AQL_queries, please change update obo script to create and update the expression_cluster obo based on this file. AQL query used to generate file is: select a, a->description, a->reference, a->remark from a in class expression_cluster, updated /home/azurebrd/public_html/cgi-bin/forms/generic.cgi to have updateVariationObo populate based on this data. Karen, verify that this looks okay in the OA, it looks fine -k, then we'll need TODO sync up /home/azurebrd/public_html/cgi-bin/forms/generic.cgi to tazendra -- J DONE, the next time you run it with wget from acedb account commandline on tazendra it will update, or the next time the cronjob picks it up -- J
  • Anatomy_term -- anat_term -- multi-ontology autocomplete on name; term info- name, WBbt ID
  • Life_stage -- lifestage -- multi-ontology autocomplete on name; term info- name
  • GO_term -- goid --, -Move to TAB2, below Life Stage, moved, multi-ontology autocomplete on name and synonym; term info -description
  • Molecule -- molecule -- multi-ontology autocomplete on name and synonym; term info- molecule ID, name, synonym
  • Phenotype -- phenotype --, -Move to TAB2 below Molecule, moved, multi-ontology, autocomplete on name and synonym; term info -description
  • Taxon --taxon--, -MOVE to bottom of TAB2, moved, multi-ontology of NCBITaxonomy ID, autocomplete on species name text until your file is ready for obo_ table -- J sent the file to you today, --k please let me know where the file is on tazendra or mangolassi, also some columns don't have a value for col2. we just store column 2 in postgres ? /home/acedb/karen/processOA/species_taxon.txt id is name, store name, synonym is taxon ID -- J TODO when live : /home/postgres/work/pgpopulation/pro_process/create_obo_taxon.pl to make the obo tables for taxon data DONE, Karen runs /home/acedb/karen/processOA/update_obo_taxon.pl to populate data based on species_taxon.txt, ran the script, the taxon ontology was not populated. -k ; 1/12/12 J changed id to id and name to taxon name., works fine -k, Didn't see script on tazendra, trasferred there for live running. Haven't run it myself, go ahead when ready -- J, moved species_taxon.txt to tazendra, ran it -k

TAB3

  • Gene -- wbgene -- -Move to top of TAB3, moved, multi-ontology, autocomplete on public_name; term info- name, WBGeneID, WBProcess, same as paper comment -- J, leave as is -k
  • Interaction -- interaction -- -Move to TAB3, below Gene, moved, multi-ontology, autocomplete on interactionID, term info- WBPaperID, all interactors, and interaction type. already exists in interaction OA, talk to the interaction curator to change autocomplete or what-not (and tell them to email me or sign this wiki) -- J changed from autocomplete on gene to autocomplete on interaction, does this still need me to talk to the interaction curator?--k, You two are the only curators using the interaction autocomplete, so if it's working correctly, that's good, if it's not, talk to her and either have her tell me what to do or that she's okay with me doing whatever you want with it, as long as it keeps storing the IDs it shouldn't mess up postgres -- J, she signed off on it, How many of these have multiple pgids ? I have to do things differently depending on how many. Also if there's multiples, how do you want to display all the things below, given that for any given table, there would be different pgids ? This is pretty complicated, I don't think the list below (while good) is good enough, a couple of examples about some Interactions with multiple IDs / multiple data types and how they should show in the Term Info would help. You often want things more complicated than other people, and while that's fine, it requires a lot more discussion on the details and the assumptions (I think there's too many assumptions here) -- J, I am asking for something that seems very simple to me, if it is too complicated we can just forget the term info stuff. please just leave the field as is (multiontology) and forget pulling over any term info-karen, strife ensued due to confusion as to there being multiple pgids per interactionID, which would have been very messy and is the case for gene_regulation, so watch out if you need term info from those tables, changes made, please confirm that term info is okay. I hope we don't ever change this, it's a lot of bulky code and hard to read -- J, it looks fine, thanks for your efforts -k, cool, should be live now -- J, looks good! Thanks. -k
    • 1/12/12 Autocomplete works, but term info needs to show interaction data =>
      • interactionID
      • paper- comma separated if many
      • interaction type
      • effector gene- locus or if no locus then WBGeneID- if many genes then comma separated
      • effector variation- name if no name then WBVarID- if many variation then comma separated
      • effector transgene name - comma separated if many
      • effector transgene gene -locus or if no locus then WBGeneID- comma separated if many
      • effector other type
      • effector other - comma separated if many -- this is a text field, it will just show that there is
      • effected gene- locus or if no locus then WBGeneID- if many genes then comma separated
      • effected variation- name if no name then WBVarID- if many variation then comma separated
      • effected transgene name - comma separated if many
      • effected transgene gene -locus or if no locus then WBGeneID- comma separated if many
      • effected other type
      • effected other - comma separated if many -- this is a text field, it will just show that there is
      • phenotype- name and WBPhenotypeID, comma separated if many
      • Remark
      • curator


  • Human_disease -- humdisease -- multi-ontology autocomplete on name and synonym (does one exist?) text until your file is ready for obo_ table -- J
  • Picture -- picture -- multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, expr
  • Movie -- movie -- multi-ontology autocomplete on ID doesn't exist yet text until your file is ready for obo_ table -- J
  • Pathway Database --pathwaydb -- ontology autocomplete on name text until your file is ready for obo_ table -- J
  • Pathway accession -- pathwayacc -- text


--kjy 19:11, 13 June 2012 (UTC)

Process Model

?WBProcess	Name  ?Text
		Summary ?Text #Evidence
		Process_name ?Text  
		Other_name ?Text
		Related_process ?WBProcess XREF Related_process
		Taxon	NCBITaxonomyID ?Text
		Involved_entity		Gene ?Gene XREF WBProcess #Evidence  
					Expression_cluster ?Expression_cluster XREF WBProcess  #Evidence
					Interaction ?Interaction XREF WBProcess #Evidence
					Anatomy_term ?Anatomy_term XREF WBProcess #Evidence
					Life_stage ?Life_stage XREF WBProcess #Evidence  
                                       Molecule ?Molecule XREF WBProcess #Evidence 
		Associated_with		Phenotype ?Phenotype XREF WBProcess #Evidence
  					GO_term ?GO_term  #Evidence
		Picture ?Picture #Evidence
		Movie ?Movie  #Evidence
		Pathway DB_info Database ?Database ?Database_field ?Accession_number //Can be used for any pathway db with unique accessionIDs
		Remark ?Text #Evidence
		Reference ?Paper XREF WBProcess


Other models effected: 

?Gene     WBProcess ?WBProcess XREF Gene #Evidence 
?Expression_cluster	 WBProcess ?WBProcess XREF Expression_cluster #Evidence 
?Interaction 	WBProcess ?WBProcess XREF Interaction
?Anatomy_term	WBProcess ?WBProcess XREF Anatomy_term
?Life_stage	WBProcess ?WBProcess XREF Life_stage 
?Molecule       WBProcess ?WBProcess XREF Molecule
?Phenotype	Associated_with WBProcess ?WBProcess XREF Phenotype 
?Picture        WBProcess ?WBProcess XREF Picture
?Movie          WBProcess ?WBProcess XREF ?Movie
?Paper	Refers_to  WBProcess ?WBProcess XREF Reference \\

Process.ace Dumper

bitbucket page: https://bitbucket.org/kyook/ky_wbprojects/wiki/edit/Process_pages
.ace dump constraints: the following must be true

  • Unique WBProcessID
  • Unique Process name
  • Curator not blank
  • Process summary not blank


--kjy 20:28, 24 February 2012 (UTC)

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