Difference between revisions of "Gene Interaction/archive"
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**To run : ./parse_ace_interaction_oa.pl gary_RNAi.ace WBPerson1823 | **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. | ** where gary_RNAi.ace is the <inputfile>,the first argument, and WBPerson# is the second argument. | ||
+ | |||
+ | |||
+ | |||
+ | ===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 Interactions]] | ||
+ | |||
+ | ====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 |
Revision as of 23:09, 18 September 2014
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.
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