Difference between revisions of "Gene Interaction"
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***'''In new OA, this field will be called "Affected Gene(s)" -- C If non-directional is on, move to non-directional gene, otherwise leave here''' | ***'''In new OA, this field will be called "Affected Gene(s)" -- C If non-directional is on, move to non-directional gene, otherwise leave here''' | ||
**Effected Variation //WBGene, WBVar, multiontology, autocomplete on Variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar" | **Effected Variation //WBGene, WBVar, multiontology, autocomplete on Variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar" | ||
− | ***'''In new OA, all variations will go into the Variation(s) field''' | + | ***'''In new OA, all variations will go into the Variation(s) field. merge both effector + effected.''' |
**Effected Transgene_Name //ontology, autocomplete transgene object name, eg iaIs3. | **Effected Transgene_Name //ontology, autocomplete transgene object name, eg iaIs3. | ||
− | ***'''In new OA, all transgenes will go into the Transgene(s) field''' | + | ***'''In new OA, all transgenes will go into the Transgene(s) field. merge both effector + effected.''' |
**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 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. | ||
***'''In new OA, all transgenes will automatically be mapped to their associated genes''' | ***'''In new OA, all transgenes will automatically be mapped to their associated genes''' | ||
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***'''In new OA, these genes will all go in the "Effector Gene(s)" field. If non-directional is on, move to non-directional gene, otherwise leave here''' | ***'''In new OA, these genes will all go in the "Effector Gene(s)" field. If non-directional is on, move to non-directional gene, otherwise leave here''' | ||
**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 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. | ||
− | ***'''In new OA, all variations will go into the Variation(s) field''' | + | ***'''In new OA, all variations will go into the Variation(s) field. merge both effector + effected.''' |
**Effector Transgene_Name //autocomplete name, ontology | **Effector Transgene_Name //autocomplete name, ontology | ||
− | ***'''In new OA, all transgenes will go into the Transgene(s) field''' | + | ***'''In new OA, all transgenes will go into the Transgene(s) field. merge both effector + effected.''' |
**Effector Transgene_Gene // autocomplete WBGene, multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id. | **Effector Transgene_Gene // autocomplete WBGene, multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id. | ||
***'''In new OA, all transgenes will automatically be mapped to their associated genes''' | ***'''In new OA, all transgenes will automatically be mapped to their associated genes''' |
Revision as of 22:20, 5 April 2012
'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
The current ?Interaction model now consolidates ?Gene_regulation objects, ?YH objects, and ?Interaction objects into a single class, ?Interaction. The proposed ?Physical_interaction model has also been consolidated into this larger model. Note that #Interaction_info and #Interaction_type have been deprecated.
?Interaction Interaction_type Physical Predicted Regulatory Change_of_localization // Indicates regulation of localization Change_of_expression_level // Indicates regulation of expression level (RNA, protein) Genetic Genetic_interaction // Indicates a generic genetic interaction that may not be accurately captured by any other term Negative_genetic // General case in which one genetic perturbation exacerbates the effects of second perturbation Synthetic // Two genetic perturbations are individually wild type but produce a phenotype when combined Enhancement // One genetic perturbation exacerbates the effects of second perturbation Unilateral_enhancement // One genetic perturbation exacerbates the effects of a second perturbation, which is otherwise wild type Mutual_enhancement // Two genetic perturbations individually result in a phenotype and combine to result in a more severe phenotype than either individual perturbation Suppression // One genetic perturbation suppresses the effects of second perturbation Unilateral_suppression // One genetic perturbation suppresses the effects of second perturbation, which is otherwise wild type Mutual_suppression // Two genetic perturbations individually result in a phenotype and combine to result in a less severe phenotype than either individual perturbation Asynthetic // Two genetic perturbations individually result in an identical phenotype which is also identical to the phenotype of their combination Suppression_enhancement // A double genetic perturbation yields a phenotype intermediate to that of either individual perturbation Epistasis // The phenotype of one genetic perturbation masks the phenotype of a second perturbation Maximal_epistasis // The more severe phenotype exhibited by two genetic perturbations is observed when both perturbations are combined Minimal_epistasis // The less severe phenotype exhibited by two genetic perturbations is observed when both perturbations are combined Suppression_epistasis // One genetic perturbation results in a phenotype which is suppressed back to wild type when combined with a second (wild type) perturbation Agonistic_epistasis // Combined phenotype is identical to the the single perturbation which is closer to the expected phenotype as determined by the neutrality function Antagonistic_epistasis // Two genetic perturbations each result in opposite phenotypes and the combined phenotype is identical to the the single perturbation which is furthest from the expected phenotype as determined by the neutrality function Oversuppression // One genetic perturbation suppresses the phenotype of a second perturbation beyond wild type (producing an opposite phenotype) Unilateral_oversuppression // One genetic perturbation suppresses the phenotype of a second (wild type) perturbation beyond wild type (producing an opposite phenotype) Mutual_oversuppression // Two genetic perturbations individually result in a similar phenotype but result in an opposite phenotype when combined Complex_oversuppression // Two genetic perturbations each result in opposite phenotypes and the combined phenotype is (relative to expectation) suppressed beyond wild type, resulting in a phenotype opposite to that expected Oversuppression_enhancement // Two genetic perturbations each result in opposite phenotypes and the combined phenotype is oversuppressed relative to one perturbation and enhanced relative to the other perturbation Phenotype_bias // " is less severe than either original phenotype, but deviates from expectation Biased_suppression // Two genetic perturbations each result in opposite phenotypes and the combined phenotype is less severe than either original phenotype, and less severe than expected Biased_enhancement // Two genetic perturbations each result in opposite phenotypes and the combined phenotype is less severe than either original phenotype, but more severe than expected Complex_phenotype_bias // Two genetic perturbations each result in opposite phenotypes, and although the combined phenotype is expected to be wild type, the actual combined perturbations result in a phenotype less severe than either original phenotype No_interaction // Negative data; no interaction was observed after testing Interactor PCR_interactor UNIQUE ?PCR_product #Interactor_info // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments Sequence_interactor UNIQUE ?Sequence #Interactor_info // Sequence of the interacting gene or protein Interactor_overlapping_CDS ?CDS #Interactor_info // CDS of the interacting gene or protein (or related sequence) Interactor_overlapping_gene ?Gene XREF Interaction #Interactor_info // Gene (or portion of gene) involved in the interaction Interactor_overlapping_protein ?Protein XREF Interaction #Interactor_info // Protein (or portion of protein) involved in the interaction Molecule_regulator ?Molecule XREF Interaction #Interactor_info // Molecule that regulates a gene or protein (ported from Gene_regulation class) Other_regulator ?Text #Interactor_info // Free text describing a regulator entity or condition that does not fall into a standard WormBase category Other_regulated ?Text #Interactor_info // Free text describing a regulated entity or condition that does not fall into a standard WormBase category Interaction_summary ?Text #Evidence Detection_method Affinity_capture_luminescence // A physical interaction detection technique Affinity_capture_MS // A physical interaction detection technique Affinity_capture_RNA // A physical interaction detection technique Affinity_capture_Western // A physical interaction detection technique Cofractionation // A physical interaction detection technique Colocalization // A physical interaction detection technique Copurification // A physical interaction detection technique Fluorescence_resonance_energy_transfer // A physical interaction detection technique Protein_fragment_complementation_assay // A physical interaction detection technique Yeast_two_hybrid // A physical interaction detection technique (Protein-protein) Biochemical_activity // A physical interaction detection technique Cocrystal_structure // A physical interaction detection technique Far_western // A physical interaction detection technique Protein_peptide // A physical interaction detection technique Protein_RNA // A physical interaction detection technique Reconstituted_complex // A physical interaction detection technique Yeast_one_hybrid // A physical interaction detection technique (Protein-DNA) Directed_yeast_one_hybrid // A physical interaction detection technique (Protein-DNA) Antibody // A regulatory interaction detection technique; Antibody name and details captured in Interactor_info hash Reporter_gene ?Text // A regulatory interaction detection technique Transgene // A regulatory interaction detection technique; Trasnsgene name and details captured in Interactor_info hash In_situ Text // A regulatory interaction detection technique Northern Text // A regulatory interaction detection technique Western Text // A regulatory interaction detection technique RT_PCR Text // A regulatory interaction detection technique Other_method ?Text // A regulatory interaction detection technique //Physical interaction-specific tag Library_info Library_screened Text INT // In the context of Yeast Two Hybrid or Yeast One Hybrid screens, for example, the library may have been cDNA library or some other pool of clones Origin From_laboratory UNIQUE ?Laboratory // A library generated at an academic laboratory From_company UNIQUE ?Text // A library generated at a company //Genetic interaction-specific tags Deviation_from_expectation Text // A text description of the way in which the phenotype deviated from expectation in genetic interactions Neutrality_function UNIQUE Multiplicative // The multiplicative neutrality function defines expectation as the product of two quantified phenotypes (relative to wild type) Additive // The additive neutrality function defines expectation as the sum of two quantified phenotypes (relative to wild type) Minimal // The minimal neutrality function defines expectation as the most severe of two quantified phenotypes (relative to wild type) //Gene regulation-specific tags Regulation_level Transcriptional // Regulation occurs at the transcriptional level Post_transcriptional // Regulation occurs at the post-transcriptional level Post_translational // Regulation occurs at the post-translational level Interaction_associated_feature ?Feature XREF Associated_with_gene_regulation #Evidence //to curate sequence feature connection [ar2] Regulation_result Positive_regulate #GR_condition Negative_regulate #GR_condition Does_not_regulate #GR_condition // added to capture negative data [040220 krb] //General tags Confidence Description Text // Free text description of the confidence, e.g. "Core" vs "Noncore" (Vidal Interactome terms) P_value UNIQUE Float // P-value confidence of interaction, if given Log_likelihood_score UNIQUE Float // Only used for Predicted interactions Throughput UNIQUE High_throughput //See BioGRID curation criteria for discussion: http://www.yeastgenome.org/help/BiogridCuration.html Low_throughput Interaction_RNAi ?RNAi XREF Interaction // RNAi experiment associated with the interaction Interaction_phenotype ?Phenotype XREF Interaction // Phenotype associated with a genetic interaction WBProcess ?WBProcess XREF Interaction // WormBase biological process associated with the interaction DB_info Database ?Database ?Database_field ?Accession_number // Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome Paper ?Paper XREF Interaction Remark ?Text #Evidence
#Interactor_info Interactor_type Non_directional // An interactor that has no inherent directionality Bait // The interactor of interest or focus; the focus/starting point of an interaction screen Target // The discovered interactor; interactors found as a result of an interaction screen Effector // In a genetic interaction, the perturbation that affects the phenotype of the other perturbation Affected // In a genetic interaction, the perturbation whose phenotype is affected by the other perturbation Trans_regulator // A trans-acting regulator, e.g. a transcription factor Cis_regulator // A cis-acting regulator, e.g. an enhancer element Trans_regulated // A gene regulated in trans, e.g. by a transcription factor Cis_regulated // A gene regulated in cis, e.g. by an enhancer element Expr_pattern ?Expr_pattern // An expression pattern altered to indicate Variation ?Variation XREF Interactor // (allele, polymorphism, etc.) involved in the interaction //removed XREF from proposal Transgene ?Transgene XREF Interactor // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal Antibody ?Text // Antibody used to detect a regulation event Antibody_info ?Antibody XREF Interactor // Free text description of the antibody used to detect a regulation event //removed XREF from proposal Remark ?Text #Evidence // Info about reagents that the model can't capture (e.g. co_suppression, RNA_reagent, etc.)
In the adoption of this new ?Interaction model in WS231, we have consolidated the ?YH and ?Gene_regulation class into the ?Interaction class. As of WS231, there were 3831 ?Gene_regulation objects, which were then converted to ?Interaction objects with IDs WBInteraction000501384 through WBInteraction000505214. As of WS231, there were 11,993 ?YH objects, which were then converted to ?Interaction objects with IDs WBInteraction000505215 through WBInteraction000517207.
Old 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
Physical Interaction Model v1.3
?Physical_interaction Evidence #Evidence Interactor Non_directional_interactor PCR_non_directional_interactor UNIQUE ?PCR_product XREF to? ?Species Sequence_non_directional_interactor UNIQUE ?Sequence XREF to? ?Species Non_directional_interactor_overlapping_CDS ?CDS XREF to? ?Species #Evidence Non_directional_interactor_overlapping_gene ?Gene XREF to ? ?Species #Evidence Non_directional_interactor_DB_info ?Database ?Database_field UNIQUE ?Accession_number //BioGRID, BioGRIDID, Numerical Value Bait PCR_bait UNIQUE ?PCR_product XREF to? ?Species Sequence_bait UNIQUE ?Sequence XREF to? ?Species Bait_overlapping_CDS ?CDS XREF to? ?Species #Evidence Bait_overlapping_gene ?Gene XREF to? ?Species #Evidence Bait_DB_info ?Database ?Database_field UNIQUE ?Accession_number //BioGRID, BioGRIDID, Numerical Value Target PCR_target UNIQUE ?PCR_product XREF to? ?Species Sequence_target UNIQUE ?Sequence XREF to? ?Species Target_overlapping_CDS ?CDS XREF to? ?Species #Evidence Target_overlapping_gene ?Gene XREF to? ?Species #Evidence Target_DB_info ?Database ?Database_field UNIQUE ?Accession_number //BioGRID, BioGRIDID, Numerical Value Experimental_System UNIQUE Affinity_capture-luminescence //Experimental_system includes WormBase tags values as well as BioGRID values 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 //BioGRID is not curating protein-DNA interactions. WB has both Y1H data and GO MF data. Directed_Y1H Text Protein_DNA Throughput UNIQUE High_throughput //See BioGRID curation criteria for discussion: http://www.yeastgenome.org/help/BiogridCuration.html Low_throughput Library_info Library_screened UNIQUE ?Library //This could also just be ?Text. Doesn't look like ?Library class is used. Origin 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 ?Text //Not currently captured by BioGRID, but this tag can accommodate the legacy YH data. Paper ?Paper XREF to ? Remark ?Text #Evidence //How would remarks coming from BioGRID be attributed? Person_evidence? Curator_confirmed? Accession_evidence? Person or Curator would require a change to the dumping file from BioGRID.
Physical Interaction Model v1.2
The revised v1 includes: 1) a ?Species tag, 2) a slot to capture Non-directional interactors (for curating things like protein complexes purified over sedimentation gradients, i.e. where there is no clear Bait or Target directionality), and 3) change ?Confidence from a specific list of phrases or statistical methods to a ?Text tag since this information is expressed in many different ways in the literature so including specific text here doesn't seem practical. If we change this to ?Text, then I'd also remove the specific Interactome_core tag.
Also, current XREF tags in the ?YH model are YH_bait and YH_target. What would be a more appropriate name? Model below has Interaction_target, etc. but I think that's not clear enough. What about Physical_interaction_target?
Also, CDS and Gene, when overlapping, have #Evidence, but the PCR and Sequence do not. Why is this? Does it have to do with needing to indicate how a CDS or Gene was selected without a corresponding sequence?
?Physical_interaction Evidence #Evidence Species UNIQUE ?Species Interactor Non_directional_interactor PCR_non_directional_interactor UNIQUE ?PCR_product XREF ? Sequence_non_directional_interactor UNIQUE ?Sequence XREF ? Non_directional_interactor_overlapping_CDS ?CDS XREF ? #Evidence Non_directional_interactor_overlapping_gene ?Gene XREF ? #Evidence Bait PCR_bait UNIQUE ?PCR_product XREF ? Sequence_bait UNIQUE ?Sequence XREF ? Bait_overlapping_CDS ?CDS XREF ? #Evidence Bait_overlapping_gene ?Gene XREF ? #Evidence Target PCR_target UNIQUE ?PCR_product XREF ? Sequence_target UNIQUE ?Sequence XREF ? Target_overlapping_CDS ?CDS XREF ? #Evidence Target_overlapping_gene ?Gene XREF ? #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 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 ?Text //This can accommodate the great variety of language used to expressed this, if curated. Paper ?Paper XREF Interaction //Should this XREF also be updated to Physical_interaction? Remark ?Text #Evidence
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 Same in new OA
- Interaction ID
- A new interaction ID is generated 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. This is for curators who would like to use 'Duplicate' to generate new objects with similar field entries and erase the Interaction IDs to let the cron job add new IDs overnight.
- interaction field autocompletes now key off of the int_index table used by the interaction_ticket.cgi, it no longer keys off of the int_name table from this field in the interaction OA, which makes the rest of this line obsolete. (OBSOLETE 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. end obsolete)
- Non_directional In new OA, there will be a separate field for each interactor type: Gene, Sequence, CDS, PCR_Product, or Protein. Since "old" interaction objects only contain genes, any genes that are part of Interaction obejcts in which the Non_directional toggle was activated will need to move to the "Non-directional Gene(s)" field. if toggle is on, move all effector + effected genes to the new non-directional gene field. get rid of this field in new OA
- 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
- In the new OA, these 11 types will be mapped as follows:
- "Genetic" will become "Genetic - Genetic Interaction"
- "Regulatory" will remain "Regulatory"
- "No_interaction" will become "Genetic - No_interaction"
- "Predicted_interaction" will become "Predicted"
- "Physical_interaction" will become "Physical"
- "Suppression" will become "Genetic - Suppression"
- "Enhancement" will become "Genetic - Enhancement"
- "Synthetic" will become "Genetic - Synthetic"
- "Epistasis" will become "Genetic - Epistasis"
- "Mutual_enhancement" will become "Genetic - Mutual_enhancement"
- "Mutual_suppression" will become "Genetic - Mutual_suppression"
- Effected Gene //autocomplete WBGene, multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
- In new OA, this field will be called "Affected Gene(s)" -- C If non-directional is on, move to non-directional gene, otherwise leave here
- Effected Variation //WBGene, WBVar, multiontology, autocomplete on Variation, store in separate lines ->.ace, Interactor "WBGene" Variation "WBVar"
- In new OA, all variations will go into the Variation(s) field. merge both effector + effected.
- Effected Transgene_Name //ontology, autocomplete transgene object name, eg iaIs3.
- In new OA, all transgenes will go into the Transgene(s) field. merge both effector + effected.
- 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.
- In new OA, all transgenes will automatically be mapped to their associated genes
- Effected Other Type //dropdown list of 'Chemicals' and 'Transgene'
- In new OA, these will be moved to the Remark
- 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.
- In new OA, these will be moved to the Remark
- Effector Gene //autocomplete WBGene, multiontology. corresponding to interactor in .ace file. order does not matter when dump to interactors
- In new OA, these genes will all go in the "Effector Gene(s)" field. If non-directional is on, move to non-directional gene, otherwise leave here
- 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.
- In new OA, all variations will go into the Variation(s) field. merge both effector + effected.
- Effector Transgene_Name //autocomplete name, ontology
- In new OA, all transgenes will go into the Transgene(s) field. merge both effector + effected.
- Effector Transgene_Gene // autocomplete WBGene, multi-ontology, ->.ace, Interactor "WBGene" Transgene "id". In case of multi genes, WBGene is followed by same transgene id.
- In new OA, all transgenes will automatically be mapped to their associated genes
- Effector Other Type //dropdown list of 'Chemicals' and 'Transgene'
- In new OA, these will be moved to the Remark
- Effector Other //free text field
- two fields above will be dumped in remark field.
- In new OA, these will be moved to the Remark
- Effected Gene //autocomplete WBGene, multiontology, corresponding to interactor in .ace file. order does not matter when dump to interactors
Note: Gene, Variation, and Transgene_Gene all refer to different genes. There is no pairing problem.
- Tab 2
- Curator//dropdown list Same in new OA
- Paper//ontology Same in new OA
- RNAi ID//free text fiel In new OA, this RNAi object will fill the "Interaction RNAi" field
- Phenotype//multiontology In new OA, this Phenotype object will fill the "Interaction phenotype" field
- Remark//big text Same in new OA
- Sentence ID//sentence shows in term info Same in new OA
- False Positive//toggle, will not give an id or no dump if the sentence is false positive, containing no interaction info Same in new OA
.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 changed the dumper to ignore line breaks and double spaces in remark field for dumping ace file
- 2011.1.27
The new Interaction OA, March 2012
- Tab1
- PGID
- Interaction ID
- Curator - Curator
- Process - ?WBProcess (MultiOntology)
- Database - ?Database ?Database_field ?Accession_number
- Paper - ?Paper
- Interaction Type - Text (Multiple-Dropdown)
- The options for Interaction Type will include:
- Physical
- Predicted
- Genetic - Genetic interaction
- Genetic - Negative genetic
- Genetic - Synthetic
- Genetic - Enhancement
- Genetic - Unilateral enhancement
- Genetic - Mutual enhancement
- Genetic - Suppression
- Genetic - Unilateral suppression
- Genetic - Mutual suppression
- Genetic - Asynthetic
- Genetic - Suppression/Enhancement
- Genetic - Epistasis
- Genetic - Maximal epistasis
- Genetic - Minimal epistasis
- Genetic - Suppression/Epistasis
- Genetic - Agonistic epistasis
- Genetic - Antagonistic epistasis
- Genetic - Oversuppression
- Genetic - Unilateral oversuppression
- Genetic - Mutual oversuppression
- Genetic - Complex oversuppression
- Genetic - Oversuppression/Enhancement
- Genetic - Phenotype bias
- Genetic - Biased suppression
- Genetic - Biased enhancement
- Genetic - Complex phenotype bias
- Genetic - No interaction
- The options for Interaction Type will include:
- Interaction Summary - Big Text
- Remark - Big text
- Tab2
- Physical interaction detection method (Multi-dropdown)
- The detection method options are:
- Affinity capture luminescence
- Affinity capture MS
- Affinity capture RNA
- Affinity capture Western
- Biochemical activity
- Cocrystal structure
- Cofractionation
- Colocalization
- Copurification
- Far western
- Fluorescence resonance energy transfer
- Protein fragment complementation assay
- Protein peptide
- Protein RNA
- Reconstituted complex
- Yeast two hybrid
- Chromatin IP
- Yeast one hybrid
- Directed yeast one hybrid
- The detection method options are:
- Library screened - Text Text (First text then an integer)
- From Laboratory - ?Laboratory (ontology)
- From Company - Text
- PCR Bait - ?PCR_product (Ontology)
- PCR Target(s) - ?PCR_product (MultiOntology)
- Non-directional PCR(s) - ?PCR_product (MultiOntology)
- Sequence Bait - ?Sequence (Ontology)
- Sequence Target(s) - ?Sequence (MultiOntology)
- Non-directional Sequence(s) - ?Sequence (MultiOntology)
- Bait overlapping CDS - ?CDS (Ontology)
- Target overlapping CDS(s) - ?CDS (MultiOntology)
- Non-directional overlapping CDS(s) - ?CDS (MultiOntology)
- Bait overlapping protein - ?Protein (Ontology)
- Target overlapping protein(s) - ?Protein (MultiOntology)
- Non-directional overlapping protein(s) - ?Protein (MultiOntology)
- Bait overlapping gene - ?Gene (Ontology)
- Target overlapping gene(s) - ?Gene (MultiOntology)
- Antibody - ?Antibody (MultiOntology)
- Antibody remark - Big Text
- Physical interaction detection method (Multi-dropdown)
- Tab3
- Non-directional Gene(s) - ?Gene (MultiOntology)
- Effector Gene(s) - ?Gene (MultiOntology)
- Affected Gene(s) - ?Gene (MultiOntology)
- Deviation from expectation - Big text
- Neutrality function - (Dropdown) options are: Multiplicative, Additive, Minimal
- Interaction RNAi - ?RNAi (Ontology)
- Interaction phenotype(s) - ?Phenotype (MultiOntology)
- Expression pattern(s) - ?Expr_pattern (MultiOntology)
- Variation(s) - ?Variation (MultiOntology)
- Transgene(s) - ?Transgene (MultiOntology)
- Tab4
- Confidence description - Text
- P-value - Text (Float)
- Log-likelihood score - Text (Float)
- Throughput - (Dropdown) options are: High throughput, Low throughput
- 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