Gene Interaction
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Revision as of 22:29, 4 May 2011 by Xdwang (talk | contribs) (→Some Notes for gene_gene_interaction)
'links to relevant pages
Caltech documentation
Interaction
OA link
Contents
Interaction Curation
Pipeline
semi-automatic curation with textpresso extracted sentences
- There are 2138 sentences (actually 2133 sentences) in the sourcefile /home/postgres/work/pgpopulation/genegeneinteraction/20091002-xiaodong/ggi_20091002
- paper starts at WBPaper00028425, ends at WBPaper00035225
- .ace dumper at /home/acedb/xiaodong/gene_gene_interaction/dump_ggi_ace.pl
- go to the directory and do: ./dump_ggi_ace.pl > some_file.ace
- Populate textpresso data in tazendra OA: done on 20110110 -X**
- cd to directory on tazendra: /home/acedb/xiaodong/textpresso_ggi
- mkdir directionay_name (eg 20110106)
- cd directory_name (eg 20110106)
- get Arun's result file (35225-35725.txt in the directory)
- run script: ./populate_textpresso_ggi_to_OA.pl 20110106/35225-35725.txt WBPerson4793 > 20110106/35225-35725.pg (with first argument file_name as input file, and second argument WBPersonID, then output file)
- after running, '20110106/35225-35725.pg' should be in '20111106' directory.
upload Gary and Chris RNAi-based interaction objects into OA
- Reading file created by Igor's script into aceDB
- you can use the empty database by ssh -X citpub@spica.caltech.edu
- then cd CitaceMirror
- then type 'ts' to launch an empty acedb
- Dumping no-worry .ace file
- Then parse into OA
- scp ace file to same directory as below
- ssh acedb@tazendra.caltech.edu (directory xiaodong/interaction_ace_parsing)
- To run : ./parse_ace_interaction_oa.pl gary_RNAi.ace WBPerson1823
- where gary_RNAi.ace is the <inputfile>,the first argument, and WBPerson# is the second argument.
dump .ace file from OA for upload
- on tazendra: /home/acedb/xiaodong/oa_interactions_dumper
- run script by calling: ./use_package.pl
- error file will be spitted out in the same directory after every run. inform curators to check the errors.
Interaction Models
Current Models
?Interaction Evidence #Evidence
Interactor ?Gene XREF Interaction #Interactor_info
Interaction_type Genetic #Interaction_info
Regulatory #Interaction_info
No_interaction #Interaction_info
Predicted_interaction #Interaction_info
Physical_interaction #Interaction_info
Suppression #Interaction_info
Enhancement #Interaction_info
Synthetic #Interaction_info
Epistasis #Interaction_info
Mutual_enhancement #Interaction_info
Mutual_suppression #Interaction_info
Confidence Confidence_level UNIQUE Float
P_value UNIQUE Float
Log_likelihood_score UNIQUE Float
Paper ?Paper XREF Interaction
DB_info Database ?Database ?Database_field ?Accession_number
Remark ?Text #Evidence
#Interactor_info
Variation ?Variation XREF Interactor
Transgene ?Transgene XREF Interactor
Remark ?Text #Evidence //info about the reagents that the model can't capture goes here (e.g. co_suppression, RNA_reagent, etc.)
#Interaction_info
Interaction_RNAi ?RNAi XREF Interaction
Effector ?Gene //master, upstream
Effected ?Gene //subject, downstream
Non_directional ?Gene //e.g. synthetic interactions - Igor
Interaction_phenotype ?Phenotype XREF Interaction
Confidence Confidence_level UNIQUE Float
P_value UNIQUE Float
#Interaction_type
Genetic //directional and non_directional
Physical_interaction
Regulation
No_interaction
Synthetic//non_directional
Epistasis
Enhancement
Suppression
Predicted //addition for WeiWei, non_direactional
Mutual_enhancement//non_directional
Mutual_suprression//non_directional
///////////////////////////////////////////////////////////////////////////////////
New Model Proposals
General comment: consider changing Confidence to a ?Text of Text tag to accomodate what will likely be many different ways to describe this
Physical Interaction Model v1
This version of the model treats each instance of a physical interaction as a separate entity.
?Physical_interaction Evidence #Evidence
Interactor Bait PCR_bait UNIQUE ?PCR_product XREF Interaction_bait //Change XREF tag to Physical...
Sequence_bait UNIQUE ?Sequence XREF Interaction_bait
Bait_overlapping_CDS ?CDS XREF Interaction_bait #Evidence
Bait_overlapping_gene ?Gene XREF Interaction_bait #Evidence
Target PCR_target UNIQUE ?PCR_product XREF Interaction_target //Change Target to Hit? Also change XREF as above?
Sequence_target UNIQUE ?Sequence XREF Interaction_target
Target_overlapping_CDS ?CDS XREF Interaction_target #Evidence
Target_overlapping_gene ?Gene XREF Interaction_target #Evidence
Experiment_type Affinity_capture-luminescence
Affinity_capture-MS
Affinity_capture-RNA
Affinity_capture-Western
Co-fractionation
Co-localization
Co-purification
FRET
PCA
Two-hybrid
Biochemical_activity
Co-crystal_structure
Far_western
Protein_peptide
Protein_RNA
Reconstituted_complex
Y1H
Directed_Y1H Text
Protein_DNA
Throughput UNIQUE High_throughput //Need to define in context of physical interactions
Low_throughput //Same as above
Library_info Library UNIQUE ?Library //This could also just be ?Text. Doesn't look like ?Library class is used.
Origin Species UNIQUE ?Species
From_laboratory UNIQUE ?Laboratory //XREF by making a Reagents tag in the ?Laboratory model?
From_company UNIQUE ?Text //We don't currently have a ?Company class. Should we?
Confidence Confidence_level UNIQUE Float //Do we need this in the ?Physical_interaction model?
P_value UNIQUE Float //Same as above.
Log_likelihood_score UNIQUE Float //Same as above.
Interaction_frequency UNIQUE Int //This would hold the Int data in the existing Library_screened tag.
Interactome_type UNIQUE Interactome_core_1 //As defined in Li et al., 2004
Interactome_core_2
Interactome_core_3
Paper ?Paper XREF Interaction //Should this XREF also be updated to Physical_interaction?
Remark ?Text #Evidence
Physical Interaction Model v2
This version of the model gives a single interaction ID to two interacting entities, but each instance, or evidence for the interaction, is added in the #Interaction_info under the corresponding Experiment_type.
?Physical_interaction Evidence #Evidence
Interactor Bait PCR_bait UNIQUE ?PCR_product XREF Interaction_bait //Change XREF tag to Physical...
Sequence_bait UNIQUE ?Sequence XREF Interaction_bait
Bait_overlapping_CDS ?CDS XREF Interaction_bait #Evidence
Bait_overlapping_gene ?Gene XREF Interaction_bait #Evidence
Target PCR_target UNIQUE ?PCR_product XREF Interaction_target //Change Target to Hit? Also change XREF as above?
Sequence_target UNIQUE ?Sequence XREF Interaction_target
Target_overlapping_CDS ?CDS XREF Interaction_target #Evidence
Target_overlapping_gene ?Gene XREF Interaction_target #Evidence
Experiment_type Affinity_capture-luminescence #Interaction_info
Affinity_capture-MS #Interaction_info
Affinity_capture-RNA #Interaction_info
Affinity_capture-Western #Interaction_info
Co-fractionation #Interaction_info
Co-localization #Interaction_info
Co-purification #Interaction_info
FRET #Interaction_info
PCA #Interaction_info
Two-hybrid #Interaction_info
Biochemical_activity #Interaction_info
Co-crystal_structure #Interaction_info
Far_western #Interaction_info
Protein_peptide #Interaction_info
Protein_RNA #Interaction_info
Reconstituted_complex #Interaction_info
Y1H #Interaction_info
Directed_Y1H Text #Interaction_info
Protein_DNA #Interaction_info
Remark ?Text #Evidence
#Interaction_info Interaction_RNAi ?RNAi XREF Interaction
Effector ?Gene //master, upstream
Effected ?Gene //subject, downstream
Non_directional ?Gene //e.g. synthetic interactions - Igor
Interaction_phenotype ?Phenotype XREF Interaction
Throughput UNIQUE High_throughput
Low_throughput
Library_info Library UNIQUE ?Library
Origin Species UNIQUE ?Species
From_laboratory UNIQUE ?Laboratory
From_company ?Text
Confidence Confidence_level UNIQUE Float
P_value UNIQUE Float
Log_likelihood UNIQUE Float
Interaction_frequency UNIQUE Int
Interactome_type UNIQUE Interactome_core_1
Interactome_core_2
Interactome_noncore
Paper ?Paper XREF Interaction
Physical Interaction Model v3
This model keeps the physical interaction as part of the general ?Interaction model with the details again going into the #Interaction_info. The #Interaction_info would now contain the information about bait/hit directionality.
?Interaction Evidence #Evidence
Interactor ?Gene XREF Interaction #Interactor_info
Interaction_type Genetic #Interaction_info
Regulatory #Interaction_info
No_interaction #Interaction_info
Predicted_interaction #Interaction_info
Physical_interaction #Interaction_info
Suppression #Interaction_info
Enhancement #Interaction_info
Synthetic #Interaction_info
Epistasis #Interaction_info
Mutual_enhancement #Interaction_info
Mutual_suppression #Interaction_info
DB_info Database ?Database ?Database_field ?Accession_number
Remark ?Text #Evidence
#Interaction_info Interaction_RNAi ?RNAi XREF Interaction
Effector ?Gene //master, upstream
Effected ?Gene //subject, downstream
Bait PCR_bait UNIQUE ?PCR_product XREF Interaction_bait //Change XREF tag to Physical...
Sequence_bait UNIQUE ?Sequence XREF Interaction_bait
Bait_overlapping_CDS ?CDS XREF Interaction_bait #Evidence
Bait_overlapping_gene ?Gene XREF Interaction_bait #Evidence
Target PCR_target UNIQUE ?PCR_product XREF Interaction_target //Change Target to Hit? Also change XREF as above?
Sequence_target UNIQUE ?Sequence XREF Interaction_target
Target_overlapping_CDS ?CDS XREF Interaction_target #Evidence
Target_overlapping_gene ?Gene XREF Interaction_target #Evidence
Experiment_type Affinity_capture-luminescence
Affinity_capture-MS
Affinity_capture-RNA
Affinity_capture-Western
Co-fractionation
Co-localization
Co-purification
FRET
PCA
Two-hybrid
Biochemical_activity
Co-crystal_structure
Far_western
Protein_peptide
Protein_RNA
Reconstituted_complex
Y1H
Directed_Y1H Text
Protein_DNA
Throughput UNIQUE High_throughput
Low_throughput
Library_info Library UNIQUE ?Library //This could also just be ?Text. Doesn't look like ?Library class is used.
Origin Species UNIQUE ?Species
From_laboratory UNIQUE ?Laboratory //XREF by making a Reagents tag in the ?Laboratory model?
From_company UNIQUE ?Text //We don't currently have a ?Company class. Should we?
Confidence Confidence_level UNIQUE Float
P_value UNIQUE Float
Log_likelihood_score UNIQUE Float
Interaction_frequency UNIQUE Int //This would hold the Int data in the existing Library_screened tag.
Interactome_type UNIQUE Interactome_core_1 //As defined in Li et al., 2004
Interactome_core_2
Interactome_core_3
Paper ?Paper XREF Interaction //Should this XREF also be updated to Physical_interaction?
Remark ?Text #Evidence
Gene_gene Interaction OA
OA interface
- Tab 1
- PGID
- Interaction ID
- no interaction ID is generate by clicking on 'new'. when 'duplicate', the ID from old entry will be in the field, but need to be deleted in order to get an new ID.
- Interaction ID will be assigned by cronjob daily at 4 am.
- If you mistakenly make a typo and assign a correct ID's value to some other ID, you will _not_ be able to bring it back (because it's an ontology) without going to postgres directly and editing the int_name and int_name_hst tables by pgid (in postgres called joinkey). You'll have to note the pgid and then manually change it in postgres.
- Non_directional
- toggle OFF (default), means interaction is directional. there is effected/effector parties involve in the object.
- toggle ON (color change to red by click) means interaction is non_directional
- Interaction Type//dropdown list with 11 types showing in .ace template
- Effected Gene //autocomplete WBGene, multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
- Effected Variation //WBGene, WBVar, multiontology, autocomplete on Variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar"
- Effected Transgene_Name //ontology, autocomplete transgene object name, eg iaIs3.
- Effected Transgene_Gene // multi-ontology, autocomplete WBGene->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id. One wbgene for each .ace line ? Make sure you really want it this way, we can go with product/promoter if that's what you want, just make sure it's what you want. It matters having extra fields and scrolling and so forth. You'll see when the text fields become multi-ontology and ontology.
- Effected Other Type //dropdown list of 'Chemicals' and 'Transgene'
- Effected Other //free text field now, however, when entering chemicals make sure to enter common names followed by mesh IDs in parenthesis for later ontologinization.
- two fields above will be dumped in remark field.
- Effector Gene //autocomplete WBGene, multiontology. corresponding to interactor in .ace file. order does not matter when dump to interactors
- Effector Variation //WBGene, WBVar, autocomplete multiontology on variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar". use name server to map variation to gene, or the file Karen gave you to map variation to gene for variation OA.
- Effector Transgene_Name //autocomplete name, ontology
- Effectot Transgene_Gene // autocomplete WBGene, multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id.
- Effector Other Type //dropdown list of 'Chemicals' and 'Transgene'
- Effector Other //free text field
- two fields above will be dumped in remark field.
Note: Gene, Variation, and Transgene_Gene all refer to different genes. There is no pairing problem.
- Tab 2
- Curator//dropdown list
- Paper//ontology
- RNAi ID//free text fiel
- Phenotype//multiontology
- Remark//big text
- Sentence ID//sentence shows in term info
- False Positive//toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info
.ace template:
- Interaction : ""
- Interactor "WBGene" Variation ""
- Interactor "WBGene" Transgene ""
- Interactor "WBGene"
- Interaction_type Genetic Effector ""
- Interaction_type Genetic Effected ""
- Interaction_type Genetic Non_directional ""
- Interaction_type Genetic Interaction_RNAi ""
- Interaction_type Genetic Interaction_phenotype ""
- Interaction_type Regulatory Effector ""
- Interaction_type Regulatory Effected ""
- Interaction_type Regulatory Non_directional ""
- Interaction_type Regulatory Interaction_RNAi ""
- Interaction_type Regulatory Interaction_phenotype ""
- Interaction_type No_interaction Effector ""
- Interaction_type No_interaction Effected ""
- Interaction_type No_interaction Non_directional ""
- Interaction_type No_interaction Interaction_RNAi ""
- Interaction_type No_interaction Interaction_phenotype ""
- Interaction_type Predicted_interaction Non_directional ""
- Interaction_type Predicted_interaction Interaction_RNAi ""
- Interaction_type Predicted_interaction Interaction_phenotype ""
- Interaction_type Physical_interaction Effector ""
- Interaction_type Physical_interaction Effected ""
- Interaction_type Physical_interaction Interaction_RNAi ""
- Interaction_type Physical_interaction Interaction_phenotype ""
- Interaction_type Suppression Effector ""
- Interaction_type Suppression Effected ""
- Interaction_type Suppression Interaction_RNAi ""
- Interaction_type Suppression Interaction_phenotype ""
- Interaction_type Enhancement Effector ""
- Interaction_type Enhancement Effected ""
- Interaction_type Enhancement Interaction_RNAi ""
- Interaction_type Enhancement Interaction_phenotype ""
- Interaction_type Synthetic Non_directional ""
- Interaction_type Synthetic Interaction_RNAi ""
- Interaction_type Synthetic Interaction_phenotype ""
- Interaction_type Epistasis Effector ""
- Interaction_type Epistasis Effected ""
- Interaction_type Epistasis Interaction_RNAi ""
- Interaction_type Epistasis Interaction_phenotype ""
- Interaction_type Mutual_enhancement Non_directional ""
- Interaction_type Mutual_enhancement Interaction_RNAi ""
- Interaction_type Mutual_enhancement Interaction_phenotype ""
- Interaction_type Mutual_suppression Non_directional ""
- Interaction_type Mutual_suppression Interaction_RNAi ""
- Interaction_type Mutual_suppression Interaction_phenotype ""
- Paper ""
- Remark ""
interaction objects source file
- there are 9242 interaction objects dumped from WS220 on Monday, 10/01/2010
- Juancarlos's parse results from this file:
/home/postgres/work/pgpopulation/interaction/20101004_xiaodong_start/out
There are two interactions in postgres, but not the .ace file : In postgres, no ace WBInteraction0008637 In postgres, no ace WBInteraction0008638//will be OA
There are 1290 interactions in .ace file not in postgres (so I imagine these are what we should read in ?)//these are RNAi based interaction objects, we want to include them in OA
There are >40000 interactions that have a ticket and are in neither .ace nor postgres.//these 398,619 interactions are from two large scale papers
Also there are interaction data in postgres without an interaction ID//will be assigned id from WBInteraction0500001.
Some Notes for gene_gene_interaction
- two large scale papers
- WBPaper00027155 (Weiwei's science paper) has 23128 objects, starting from WBInteraction0008637 and ending at WBInteraction0050578 (blank ids in between)
- WBPaper00031465 (Lee's Nature Genetics paper) has 375491 objects, starting from WBInteraction 0100001, ending at WBInteraction0475491 (which is the largest WBInteraction id in acedb)
- directories on tazendra related to gene_gene_interaction (home/acedb/xiaodong)
- assigning_interaction_ids
- textpresso_ggi
- interaction_ace_parsing
- oa_interactions_dumper
- citace upload notes
- 2011.1.27
- caught-up at acedb reading: WBInteraction0500069 (Karen), new line in remark field. fixed in .ace file.
- some confusion on ids. found out ticket issuer was using sandbox data. fixed.
- 2011.5.4
- Karen needed to update variation_wbgene file on tazendra: /home/acedb/jolene/WS_AQL_queries/Variation_gene.txt
- Juancarlos change the dumper to ignore line breaks and double spaces in remark field for dumping ace file
- 2011.1.27
