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load-config-example.yaml
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load-config-example.yaml
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database_name: PomBase
db_name_for_cv: PBO
evidence_types:
IMP:
name: Inferred from Mutant Phenotype
IDA:
name: Inferred from Direct Assay
IGI:
name: Inferred from Genetic Interaction
with_gene: 1
IPI:
name: Inferred from Physical Interaction
with_gene: 1
EXP:
name: Inferred from Experiment
IEP:
name: Inferred from Expression Pattern
ISS:
name: Inferred from Sequence or Structural Similarity
ISO:
name: Inferred from Sequence Orthology
ISA:
name: Inferred from Sequence Alignment
ISM:
name: Inferred from Sequence Model
IGC:
name: Inferred from Genomic Context
IBA:
name: Inferred from Biological aspect of Ancestor
IBD:
name: Inferred from Biological aspect of Descendant
IKR:
name: Inferred from Key Residues
IRD:
name: Inferred from Rapid Divergence
RCA:
name: inferred from Reviewed Computational Analysis
NAS:
name: Non-traceable Author Statement
IC:
name: Inferred by Curator
ND:
name: No biological Data available
IEA:
name: Inferred from Electronic Annotation
NR:
name: Not Recorded
TAS:
name: Traceable Author Statement
UNK:
name: Unknown
Microscopy: ~
'Cell growth assay': ~
'Other': ~
'Other direct assay': ~
'Affinity Capture-Luminescence': ~
'Affinity Capture-MS': ~
'Affinity Capture-RNA': ~
'Affinity Capture-Western': ~
'Biochemical Activity': ~
'Chromatography evidence': ~
'Co-crystal Structure':
name: Co-crystal Structure
symmetrical: yes
'Co-fractionation':
name: Co-fractionation
symmetrical: yes
'Co-localization':
name: Co-localization
symmetrical: yes
'Co-purification':
name: Co-purification
symmetrical: yes
'Dosage Growth Defect': ~
'Dosage Lethality': ~
'Dosage Rescue': ~
'FRET':
name: FRET
'Far Western': ~
'Microarray RNA expression level data': ~
'Negative Genetic':
name: Negative Genetic
symmetrical: yes
'PCA':
name: PCA
symmetrical: yes
'Phenotypic Enhancement': ~
'Phenotypic Suppression': ~
'Positive Genetic':
name: Positive Genetic
symmetrical: yes
'Protein-RNA': ~
'Protein-peptide': ~
'Reconstituted Complex': ~
'Synthetic Growth Defect':
name: Synthetic Growth Defect
symmetrical: yes
'Synthetic Haploinsufficiency':
name: Synthetic Haploinsufficiency
symmetrical: yes
'Synthetic Lethality':
name: Synthetic Lethality
symmetrical: yes
'Synthetic Rescue': ~
'Two-hybrid': ~
'Reporter gene assay': ~
'Enzyme assay data': ~
'Flow cytometry data': ~
'Chromatin immunoprecipitation experiment': ~
'Quantitative PCR': ~
'Fusion protein localization experiment': ~
'Immunolocalization experiment data': ~
'Epitope-tagged protein immunolocalization experiment data': ~
'Protein localization experiment': ~
'Co-immunoprecipitation experiment': ~
'Electrophoretic mobility shift assay data': ~
'Northern assay evidence': ~
'Particle size and count assay': ~
'Western blot assay': ~
'Substance quantification': ~
'Substance quantification evidence': ~
'Transcript expression level evidence': ~
'Competitive growth assay evidence': ~
'Plasmid maintenance assay evidence': ~
'Sodium dodecyl sulfate polyacrylamide gel electrophoresis': ~
'FPR':
name: fitness profiling
definition: "ECO term name is 'competitive growth assay evidence' (ECO:0000336)"
'ECO:0000000':
name: evidence
definition: A type of information that is used to support an assertion.
'ECO:0000007':
name: immunofluorescence evidence
'ECO:0000049':
name: reporter gene assay evidence
'ECO:0000106':
name: Northern assay evidence
'ECO:0000112':
name: Western blot evidence
'ECO:0000124':
name: fusion protein localization evidence
'ECO:0000058':
name: expression microarray evidence
'ECO:0000336':
name: competitive growth assay evidence
'ECO:0000108':
name: reverse transcription polymerase chain reaction transcription evidence
'ECO:0000110':
name: RNA protection assay evidence
'ECO:0000048':
name: transcript expression level evidence
'ECO:0000231':
name: quantitative PCR
definition: "ECO term name is 'quantitative polymerase chain reaction evidence'"
'ECO:0000006':
name: experimental evidence
'ECO:0000337':
name: gel electrophoresis evidence
'ECO:0000221':
name: high throughput nucleotide sequencing assay evidence
'ECO:0000098':
name: in situ hybridization assay evidence
'ECO:0001096':
name: mass spectrometry evidence
'ECO:0000059':
name: experimental phenotypic evidence
'ECO:0000279':
name: western blot evidence used in manual assertion
'ECO:0005653':
name: northern assay evidence used in manual assertion
'ECO:0005660':
name: quantitative polymerase chain reaction evidence used in manual assertion
'ECO:0007087':
name: ribosome profiling evidence
'ECO:0007183':
name: protein expression level evidence based on western blot used in manual assertion
phenotype_cv_name: fission_yeast_phenotype
parental_strain:
4896: '972 h-'
cvs:
PomBase allele types:
- name: amino_acid_mutation
- name: nucleotide_mutation
- name: deletion
- name: partial_amino_acid_deletion
description: Deletion of part of a gene.
- name: partial_nucleotide_deletion
- name: nonsense_mutation
- name: wild_type
- name: unrecorded
description: An allele whose type is not apparent from the paper.
- name: unknown
description: An allele whose type has not been established.
- name: other
extension_restrictions:
fission_yeast_phenotype:
allowed:
- is_bearer_of
- has_penetrance
- assayed_using
- has_severity
- occurs_in
- occurs_at
- assayed_enzyme
- assayed_substrate
biological_process:
allowed:
- exists_during
- happens_during
- has_substrate
- requires_feature
molecular_function:
allowed:
- happens_during
cellular_component:
allowed:
- exists_during
'PSI-MOD':
allowed:
- absent_during