Difference between revisions of "Topic pages"

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*WBProcess -- wbprocess -- ontology autocomplete on process_term same as the related_process ontology ? -- J,  remove this table,  it is not necessary --k, removed -- J
 
*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  
 
*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'''
+
*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, so I'll take that as a no, do not change anything that affects anyone else. We are done with this field -k'''
  
 
TAB2
 
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. 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 ? Let me know to give write permission to your account if you'll be rewriting to it. -- J''' '''TODO when live, run /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/create_obo_tables.pl /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/populate_obo_exprcluster.pl -- J'''
+
*'''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 ''' 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 '''TODO when live, run /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/create_obo_tables.pl /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/populate_obo_exprcluster.pl -- J''' '''I just looked up a few expression clusters in the ProcessOA and it looks and works fine-k'''
 
 
 
 
  
 
*Anatomy_term -- anat_term --  multi-ontology autocomplete on name; term info- name, WBbt ID  
 
*Anatomy_term -- anat_term --  multi-ontology autocomplete on name; term info- name, WBbt ID  
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TAB3
 
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''
 
* 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'''
+
*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 itHow 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'''
 
**1/12/12 Autocomplete works, but term info needs to show interaction data =>  
 
**1/12/12 Autocomplete works, but term info needs to show interaction data =>  
 
***interaction type
 
***interaction type
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***effector transgene gene -locus or if no locus then WBGeneID- comma separated if many
 
***effector transgene gene -locus or if no locus then WBGeneID- comma separated if many
 
***effector other type
 
***effector other type
***effector other - comma separated if many '''-- this is a text field, it will just show that there is'''
+
***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 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 variation- name if no name then WBVarID- if many variation then comma separated
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***effected transgene gene -locus or if no locus then WBGeneID- comma separated if many
 
***effected transgene gene -locus or if no locus then WBGeneID- comma separated if many
 
***effected other type
 
***effected other type
***effected other - comma separated if many '''-- this is a text field, it will just show that there is'''
+
***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
 
***phenotype- name and WBPhenotypeID, comma separated if many
 
***Remark  
 
***Remark  

Revision as of 18:43, 18 January 2012

back to' Caltech documentation
Other process related pages

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

  • Metabolic pathways: BioCyc, Reactome, NemaPath (KEGG)
  • Other pathways: Reactome

Resources

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


WBProcess OA

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, so I'll take that as a no, do not change anything that affects anyone else. We are done with this field -k

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 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 TODO when live, run /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/create_obo_tables.pl /home/postgres/work/pgpopulation/obo_oa_ontologies/20120118_exprcluster/populate_obo_exprcluster.pl -- J I just looked up a few expression clusters in the ProcessOA and it looks and works fine-k
  • 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, 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.

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
    • 1/12/12 Autocomplete works, but term info needs to show interaction data =>
      • 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
      • paper- comma separated if many


  • 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