| abbreviation |
None |
| aberration |
Associated deficiency (etc.) whose breakpoint causes the mutation |
| abstract |
The author summary of the publication. From PubMed otherwise from Mod or manual reference creation. |
| abundance |
The free text describing the amount of sample used |
| acquires_in_merge |
For an entity that persists through a merge, the list of entities that it subsumes in a given NomenclatureEvent. |
| affiliated_alliance_member |
The Alliance Member the person is affiliated with |
| age |
The age at which an annotated event was observed. |
| aggregation_database |
The database that collected the interaction annotation from another resource and aggregated it into a consolidated resource, e.g. IMEx. An MITerm from the AGR aggregation database subset of MITerms. |
| aggregation_database_curie |
The database that collected the interaction annotation from another resource and aggregated it into a consolidated resource, e.g. IMEx. Value is the curie of an MITerm from the AGR aggregation database subset of MITerms. |
| agm_identifier |
None |
| agm_ingest_set |
None |
| agm_secondary_id_dtos |
None |
| agm_secondary_ids |
Secondary IDs of a given AGM |
| allele_allele_association_object |
None |
| allele_allele_associations |
None |
| allele_association_subject |
None |
| allele_cell_line_association_ingest_set |
None |
| allele_cell_line_association_object |
None |
| allele_cell_line_associations |
None |
| allele_construct_association_ingest_set |
None |
| allele_construct_association_object |
None |
| allele_construct_associations |
None |
| allele_database_status |
Database status of a given allele |
| allele_database_status_dto |
None |
| allele_full_name |
The one current full name for an allele: e.g., wg1. |
| allele_full_name_dto |
The one current full name for an allele: e.g., wg1. |
| allele_functional_impact_dtos |
None |
| allele_functional_impacts |
Functional impacts of a given allele |
| allele_gene_association_ingest_set |
None |
| allele_gene_association_object |
None |
| allele_gene_associations |
None |
| allele_generation_method_association_ingest_set |
None |
| allele_generation_method_association_object |
None |
| allele_generation_method_associations |
None |
| allele_germline_transmission_status |
Germline transmission status for a given allele |
| allele_germline_transmission_status_dto |
None |
| allele_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the allele |
| allele_image_association_ingest_set |
None |
| allele_image_association_object |
None |
| allele_image_associations |
None |
| allele_ingest_set |
None |
| allele_inheritance_mode_dtos |
One or more allele inheritance mode DTO objects to be submitted |
| allele_inheritance_modes |
Inheritance modes for an allele |
| allele_mutation_type_dtos |
None |
| allele_mutation_types |
Mutation types for a given allele |
| allele_nomenclature_event_dtos |
None |
| allele_nomenclature_events |
Nomenclature events of a given allele |
| allele_origin_association_ingest_set |
None |
| allele_origin_association_object |
None |
| allele_origin_associations |
None |
| allele_protein_association_ingest_set |
None |
| allele_protein_association_object |
None |
| allele_protein_associations |
None |
| allele_secondary_id_dtos |
None |
| allele_secondary_ids |
Secondary IDs of a given allele |
| allele_symbol |
The one current accepted symbol for the allele: e.g., wg1. |
| allele_symbol_dto |
The one current accepted symbol for the allele: e.g., wg1. |
| allele_synonym_dtos |
None |
| allele_synonyms |
Holds between an Allele and a synonym. |
| allele_transcript_association_ingest_set |
None |
| allele_transcript_association_object |
None |
| allele_transcript_associations |
None |
| allele_variant_association_ingest_set |
None |
| allele_variant_association_object |
None |
| allele_variant_associations |
None |
| alliance_member_id |
An integer referring to an AllianceMember object in the AllianceMember/MOD database table. It's a primary key in the AllianceMember/MOD table, a foreign key if used in other tables. |
| alliance_member_release_version |
Version of Alliance member/MOD release used for submitted file |
| amino_acid_reference |
reference genome amino acid sequence at variant position |
| amino_acid_variant |
variant amino acid sequence at variant position |
| analyses |
TODO: added as a result of 'origin' class - please advise on a more descriptive slot/class definition. |
| anatomical_structure |
The primary anatomical structure referred to within the context of an AnatomicalSite object. |
| anatomical_structure_curie |
The primary anatomical structure referred to within the context of an AnatomicalSite object. The range is any string representing an AnatomicalTerm ontology term |
| anatomical_structure_qualifier_curies |
None |
| anatomical_structure_qualifiers |
None |
| anatomical_structure_uberon_term_curies |
UBERON slim terms that apply to the anatomical structure. |
| anatomical_structure_uberon_terms |
UBERON slim terms that apply to the anatomical structure. |
| anatomical_substructure |
Primary anatomical substructure referenced within the context of an AnatomicalSite. |
| anatomical_substructure_curie |
Primary anatomical substructure referenced within the context of an AnatomicalSiteDTO. The range is any string representing an AnatomicalTerm ontology term. |
| anatomical_substructure_qualifier_curies |
None |
| anatomical_substructure_qualifiers |
None |
| anatomical_substructure_uberon_term_curies |
String representations of UBERON slim terms that apply to the anatomical substructure. |
| anatomical_substructure_uberon_terms |
UBERON slim terms that apply to the anatomical substructure. |
| anatomy_function |
WB specific. Allow the connection between Anatomy_term, Phenotype and gene Eg WBbtf0001 |
| ancestors |
The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like "develops_from", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship). |
| annotation_type |
The type of annotation classified according to curation method. Submitted value should be a vocabulary term from the 'Annotation types' vocabulary |
| annotation_type_name |
Name of the VocabularyTerm describing the annotation type selected from the 'Annotation types' Vocabulary |
| antibody_ingest_set |
An ingest set for Antibody objects |
| antibody_target_gene_identifiers |
Identifiers (curie/primary_external_id/mod_internal_id) of the genes whose gene products are recognized by the antibody. |
| antibody_target_genes |
The genes whose gene products are recognized by the antibody. |
| antigen_taxon |
Holds between an Antibody and the species from which the antigen originates (as represented by taxon). |
| antigen_taxon_curie |
Holds between an Antibody and the species from which the antigen originates (as represented by taxon). |
| api_token |
The API token of the LoggedInPerson for the curation system |
| assembly_component_ingest_set |
None |
| assembly_versions |
single or paired end sequencing; might be better in experiment info |
| asserted_allele |
The allele to which something is manually asserted to be associated. |
| asserted_allele_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the allele to which something is manually asserted to be associated |
| asserted_gene_identifiers |
Identifiers (curie/primary_external_id/mod_internal_id) of the gene(s) to which something is manually asserted to be associated |
| asserted_genes |
The gene(s) to which something is manually asserted to be associated. |
| associated_transcript_identifiers |
Identifiers (curie/primary_external_id/mod_internal_id) of transcript(s) associated with polypeptide to which variant is aligned. |
| associated_transcripts |
Transcript(s) associated with polypeptide to which variant is aligned. |
| association_slot |
any slot that relates an association to another entity |
| authors |
Ordered author entities for this publication. An Author is associated with only one publication. A Person can be associated with multiple publications. |
| backend_bulk_load_type |
None |
| backend_load_type |
None |
| biosample_agm |
An affected genomic model (AGM) from which a biosample has been derived |
| biosample_agm_type |
Indicates the type of AGM biosample; enum: fish, genotype, strain |
| biosample_agm_type_name |
Indicates the type of AGM biosample; enum: fish, genotype, strain |
| biosample_allele |
An allele of focus for a particular biosample |
| biosample_text |
The free text of the biosample genomic information if no biosample is available |
| birt_report_file_path |
File path to where the BIRT file has been saved |
| bulk_load |
A link back to the parent bulk load |
| bulkload_group |
Bulk load group designed to group together bulk loads |
| bulkload_status |
Status used to capture the progress of the load |
| bulkload_url |
The URL that this bulk load will download for ingest |
| calculated_cdna_end |
end position of variation in cDNA coordinates as calculated by VEP from input VCF, GFF and BAM files |
| calculated_cdna_start |
start position of variation in cDNA coordinates as calculated by VEP from input VCF, GFF and BAM files |
| calculated_cds_end |
end position of variation in CDS coordinates as calculated by VEP from input VCF, GFF and BAM files |
| calculated_cds_start |
start position of variation in CDS coordinates as calculated by VEP from input VCF, GFF and BAM files |
| calculated_protein_end |
end position of variation in protein amino acid coordinates as calculated by VEP from input VCF, GFF and BAM files |
| calculated_protein_start |
start position of variation in protein amino acid coordinates as calculated by VEP from input VCF, GFF and BAM files |
| caption |
Text describing the contents of a figure or table in a publication. |
| category |
The alliance category type. Only relevant at Alliance. |
| category_tag_names |
A list of controlled vocabulary terms to describe the experiment |
| category_tags |
A list of controlled vocabulary terms to describe the experiment |
| cds_association_subject |
Subject slot to be used for CDS associations |
| cds_genomic_location_association_object |
None |
| cds_genomic_location_associations |
None |
| cds_type |
SOTerm describing CDS type |
| cds_type_curie |
Curie of SOTerm describing CDS type |
| cell_line_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the cell line |
| cellular_component |
The primary cellular component referred to within the context of an AnatomicalSite object. |
| cellular_component_curie |
The primary cellular component referred to within the context of an AnatomicalSite object. The range is any string representing a GOTerm ontology term |
| cellular_component_other |
Is set to true when no cellular_component_ribbon_term is available |
| cellular_component_qualifier_curies |
None |
| cellular_component_qualifiers |
None |
| cellular_component_ribbon_term |
The primary cellular component slim term referred to within the context of an AnatomicalSite object and used by the expression ribbon. |
| channel_id |
for microarray experiments, channel ID |
| channel_number |
for micorarray data, which channel this sample is in, 1 or 2 |
| chemical_mutagen |
The chemical used to generate the mutation through mutagenesis |
| chemical_mutagen_name |
The name of the chemical used to generate the mutation through mutagenesis |
| child_count |
None |
| chromosome_curie |
The NCBI chromosome accession number for the chromosome. |
| chromosome_ingest_set |
None |
| clonality |
The clonality of the antibody: e.g., monoclonal. |
| clonality_name |
Name of the VocabularyTerm representing the clonality of the antibody: e.g., monoclonal. From the Antibody Clonality CV. |
| codon_reference |
reference sequence of codon(s) affected by variation - bases outside of the variant region are in lower case, those within are in upper case (e.g. cTa) |
| codon_variant |
variant sequence of codon(s) affected by variation - bases outside of the variant region are in lower case, those within are in upper case (e.g. cAa) |
| common_names |
The list of common names used for a species |
| completed_records |
The number of completed records |
| component_dtos |
None |
| component_symbol |
The free text of a symbol or name of a construct component for which no curie exists or is available |
| components |
Collection of genomic components that make up a model, i.e. 'allele', each with a zygosity |
| condition_anatomy |
None |
| condition_anatomy_curie |
Curie of AnatomicalTerm associated with condition |
| condition_chemical |
None |
| condition_chemical_curie |
Curie of ChemicalTerm associated with condition |
| condition_class |
None |
| condition_class_curie |
Curie of ZECOTerm describing condition class |
| condition_dtos |
None |
| condition_free_text |
Free-text description of the experimental condition |
| condition_gene_ontology |
None |
| condition_gene_ontology_curie |
Curie of GOTerm associated with condition |
| condition_id |
None |
| condition_id_curie |
Curie of ExperimentalConditionOntologyTerm describing condition |
| condition_quantity |
None |
| condition_relation_dtos |
None |
| condition_relation_type |
Submitted value should be a vocabulary term from the 'Condition relation types' vocabulary |
| condition_relation_type_name |
Name of VocabularyTerm from 'Condition relation types' vocabulary |
| condition_relations |
None |
| condition_summary |
A human-readable summary of the experimental condition accounting for all ontology terms and free-text components of the ExperimentalCondition object. Not generated or submitted by DQMs, but generated at the Alliance after ingest only (or generated/updated in the curation interface). |
| condition_taxon |
None |
| condition_taxon_curie |
Curie of NCBITaxonTerm associated with condition |
| conditions |
None |
| consequence |
SOTerm (child of SO:0001576 - transcript_variant) that describes the consequence of the variant, as stated in the source reference. In practice source consequence will be associated with locations at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation. |
| consequence_curie |
Curie of SOTerm (child of SO:0001576 - transcript_variant) that describes the consequence of the variant, as stated in the source reference. In practice source consequence will be associated with locations at any or all of VariantLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation. |
| construct_association_subject |
None |
| construct_component_dtos |
None |
| construct_components |
None |
| construct_full_name |
Holds between a Construct and a full name. |
| construct_full_name_dto |
Holds between a Construct and a full name. |
| construct_genomic_entity_association_ingest_set |
An ingest set for ConstructGenomicEntityAssociationDTO |
| construct_genomic_entity_association_object |
None |
| construct_genomic_entity_associations |
None |
| construct_identifier |
Either the MOD curie or internal ID that was used in the submission of the associated construct |
| construct_ingest_set |
An ingest set for Constructs |
| construct_symbol |
Holds between a Construct and the one current accepted symbol |
| construct_symbol_dto |
Holds between a Construct and the one current accepted symbol |
| construct_synonym_dtos |
Holds between a Construct and a list of synonyms. |
| construct_synonyms |
Holds between a Construct and a list of synonyms. |
| contig |
Contig or clone this gene is located to |
| copyright_date |
|
| corpus |
in-out-review corpus status of the publication at the mod. null means needs_review, false means outside_corpus, true means inside_corpus. |
| corresponding_author |
Indicates if the author is a corresponding author. |
| counter |
a number to identify an alliance resource in a subdomain |
| created_by |
The individual that created the entity. |
| created_by_curie |
Curie of the Person object representing the individual that created the entity |
| cron_schedule |
A string describing the cron syntax for the schedule |
| cropped_from |
Another larger image from which this image was cropped. |
| cross_reference |
None |
| cross_reference_dto |
None |
| cross_reference_dtos |
None |
| cross_references |
Holds between an object and its CrossReferences. |
| curated_consequence |
SOTerm that describes the consequence of the variant, as determined by the curator. In practice curated consequence will be associated with locations at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation. |
| curated_consequence_curie |
Curie of SOTerm that describes the consequence of the variant, as determined by the curator. In practice curated consequence will be associated with locations at any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation. |
| curated_variant_genomic_locations |
Location of the variant in a genomic context. multiple variant_genome_locations represent multiple assemblies. because we want the variant to stay consistent between assemblies, we must have a single variant object apart from its location. |
| curated_variant_polypeptide_locations |
Location of the variant within polypeptide entities. |
| curated_variant_transcript_locations |
Location of the variant within transcript entities. |
| curation_report |
Links a report history to its associated report |
| curation_report_group |
Links a curation report to its report group |
| curation_report_status |
Describes the status of the curation report |
| curation_report_timestamp |
Timestamp for creation of BIRT report file |
| curator_comment |
A publicly visible explanatory note from curators about some entity. |
| curie |
A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI |
| current |
None |
| current_version |
The current version of the entity, generated by this nomenclature event. It starts at one, and is incremented by one with every major change. |
| data_provider |
The organization (e.g. MOD) from which the data was sourced |
| data_provider_cross_reference |
CrossReference to the organization from which the data was sourced |
| data_provider_dto |
Ingest object representing the organization (e.g. MOD) from which the data was sourced and a CrossReference to that organisation's site |
| database_status |
Database status of the allele |
| database_status_name |
Name of the VocabularyTerm describing the database status |
| dataset_ids |
list of primary dataset ids that a sample is associated with |
| date_arrived_in_pubmed |
Day in which a reference or resource was created in PubMed. Only relevant for PubMed references. |
| date_created |
The date on which an entity was created. This can be applied to nodes or edges. |
| date_last_loaded |
Indicates when the file was last loaded |
| date_last_modified_in_pubmed |
Date on which entity was last updated at PubMed. Only relevant for PubMed references. |
| date_published |
Date on which an entity was published. From PubMed otherwise from Mod or manual reference creation. |
| date_updated |
Date on which an entity was last modified. |
| db_date_created |
The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data). |
| db_date_updated |
Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database. |
| dbkey |
Typically the primary key on the table. Should be a global sequence in the database to insure uniqueness over the entire suite of tables. Alternatively, could be a serial8 identifier. Tables with a dbkey should have an alternate key to establish uniqueness based on the data in the table. |
| default_url_template |
Default URL template for the resource |
| definition |
The explanation of the meaning of a term. |
| definition_urls |
None |
| deleted_sequence |
The sequence of DNA base pairs removed from the reference sequence by the variant. |
| descendant_count |
None |
| descendants |
The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like "develops_from", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship). |
| description |
a human-readable description of an entity |
| designating_laboratories |
A laboratory, rarely laboratories, which designated this gene |
| designating_laboratory |
A laboratory which designated this gene class |
| designating_persons |
A person/persons who designated this gene |
| detection_method |
The experimental method used to identify the physical interaction between two molecules. An MITerm from the AGR detection method subset of MITerms. |
| detection_method_curie |
The experimental method used to identify the physical interaction between two molecules. Value is the curie of an MITerm from the AGR detection method subset of MITerms. |
| detection_reagents |
Reagents used in the expression assay: e.g., construct, antibodies, probes. |
| developmental_stage_start |
The beginning developmental stage at which an annotated event was observed. |
| developmental_stage_start_curie |
The beginning developmental stage at which an annotated event was observed. |
| developmental_stage_stop |
The end developmental stage at which an annotated event was observed. This is not required if the annotation applies to a single stage. |
| developmental_stage_stop_curie |
The end developmental stage at which an annotated event was observed. This is not required if the annotation applies to a single stage. |
| disease_agm_ingest_set |
None |
| disease_allele_ingest_set |
None |
| disease_annotation_object |
The Disease Ontology term |
| disease_annotation_subject |
The biological entity to which the disease ontology term is associated. |
| disease_gene_ingest_set |
None |
| disease_genetic_modifier_agms |
Specifies an affected genomic model (e.g. genotype) that modifies a disease model. |
| disease_genetic_modifier_alleles |
Specifies an allele that modifies a disease model. |
| disease_genetic_modifier_genes |
Specifies a gene that modifies a disease model. |
| disease_genetic_modifier_identifiers |
Identifiers (curie/primary_external_id/mod_internal_id) of Gene, Allele or AGM that modifies the disease model |
| disease_genetic_modifier_relation |
A relation describing how the genetic modifier modifies the disease model. Submitted value should be a vocabulary term from the 'Disease genetic modifiers' vocabulary |
| disease_genetic_modifier_relation_name |
Name of the VocabularyTerm that describes how the genetic modifier modifies the disease model, selected from the 'Disease genetic modifier relations' Vocabulary. |
| disease_qualifier_names |
Names of terms from the 'Disease qualifiers' vocabulary |
| disease_qualifiers |
Submitted values should be vocabulary terms from the 'Disease qualifiers' Vocabulary |
| disease_relation_name |
Name of term from 'Disease Relation Vocabulary' vocabulary |
| display_name |
None |
| display_synonym |
Placeholder. |
| display_text |
A version of a synonym string for display. Any UTF8 character is permitted. |
| distance_between |
distance_between is zero for reflexive–transitive closure each node has an ancestor or descendant of itself |
| dna_mutation_type |
The type of DNA mutation, for example, insertion, deletion, substitution, or indel. |
| dna_mutation_type_curie |
Curie of SOTerm describing the type of DNA mutation, for example, insertion, deletion, substitution, or indel. |
| do_term_curie |
Curie of DOTerm describing the disease |
| editors |
holds between a resource and a editor_resource |
| emails |
list of emails for a person |
| enables |
None |
| end |
The end of the feature in positive 1-based integer coordinates relative to the reference landmark. |
| entity_assayed |
The subject of the ExpressionExperiment. This will usually be a Gene, but may be a sequence feature, or a placeholder if the exact subject of the expression pattern is unknown (e.g., unknown epitope of an antibody). |
| error_message |
Error message for curation reports |
| event_status |
Status for an event change: provisional or approved. |
| event_type |
Category of major change event for an entity. |
| evidence |
The evidence that supports some assertion. |
| evidence_code |
None |
| evidence_code_curie |
Curie of ECOTerm |
| evidence_code_curies |
List of ECOTerm curies |
| evidence_codes |
ECO term IDs |
| evidence_curies |
Curies of InformationContentEntity objects given as evidence |
| exon_association_subject |
Subject slot to be used for exon associations |
| exon_genomic_location_association_object |
None |
| exon_genomic_location_associations |
None |
| exon_number |
The exon number of the variant location. If the variant is in an intron, this slot is not populated. Primarily used for zebrafish. |
| exon_type |
SOTerm describing exon type |
| exon_type_curie |
Curie of SOTerm describing exon type |
| experiment_type |
Type of experiment by which these genes were collated eg chip-seq, interaction, expression |
| expression_annotation_image_associations |
None |
| expression_annotation_image_pane_association_object |
None |
| expression_annotation_subject |
The entity for which an expression pattern is being described; the exact type will be constrained by the type of ExpressionAnnotation. |
| expression_annotations |
The list of ExpressionAnnotations for a given ExpressionExperiment. |
| expression_assay_curie |
The assay used to experimentally determine gene expression. |
| expression_assay_used |
The assay used to experimentally determine gene expression. |
| expression_pattern |
The spatiotemporal expression pattern of the expression annotation subject. |
| expression_qualifiers |
Qualifiers that describe additional characteristics of gene expression. For example: faint, intense, restricted. |
| failed_records |
The number of failed records |
| file_size |
The size of the file |
| first |
first identifier in a range |
| first_author |
Indicates if the author is a first author. |
| first_name |
first name of a person |
| fms_data_sub_type |
The dataSubType paramater in the FMS |
| fms_data_type |
The dataType paramater in the FMS |
| format_text |
A version of a synonym string using only ASCII characters, which is easier to type (for searches), print and parse. For example, Greek characters are transliterated. |
| formula |
Formula of the molecule |
| free_text |
A free text string that describes some aspect of an entity. |
| from_image |
Holds between an ImagePane and an Image. |
| full_name |
The full name of the entity |
| full_name_renamed_from |
The previous full_name for a renamed entity. |
| full_name_renamed_to |
The new full_name for a renamed entity. |
| functional_impact_names |
Name of the VocabularyTerm describing the experimentally assessed functional impact of the allele, e.g. knockout / amorphic |
| functional_impacts |
Experimentally assessed functional impact of the allele, e.g. knockout / amorphic |
| gene_association_subject |
Subject slot to be used for gene associations |
| gene_change_events |
Change events for a given gene. |
| gene_chromosomal_location_association_object |
None |
| gene_chromosomal_location_associations |
None |
| gene_full_name |
The one current full name for a gene: e.g., wingless, paired box 2a. |
| gene_full_name_dto |
The one current full name for a gene: e.g., wingless, paired box 2a. |
| gene_gene_association_object |
the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa. |
| gene_genetic_interaction_ingest_set |
None |
| gene_genetic_map_association_object |
None |
| gene_genetic_map_positions |
None |
| gene_genomic_location_association_object |
None |
| gene_genomic_location_associations |
None |
| gene_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the gene |
| gene_ingest_set |
None |
| gene_level_consequence |
Boolean indicating whether transcript consequence is the most severe consequence for the corresponding gene. In the case of equally severe consequences, a single transcript consequence will be designated as the gene-level consequence by the VEP |
| gene_localization_type |
The type of gene localization, for example, intronic, intergenic, or intragenic. |
| gene_localization_type_curie |
Curie of SOTerm describing the type of gene localization, for example, intronic, intergenic, or intragenic. |
| gene_molecular_interaction_ingest_set |
None |
| gene_pathway_association_object |
None |
| gene_relation_name |
Name of VocabularyTerm describing relationship between a subject entity and an object Gene |
| gene_secondary_id_dtos |
None |
| gene_secondary_ids |
Secondary IDs of a given gene |
| gene_symbol |
The one current accepted symbol for a gene: e.g., wg, pax2a. |
| gene_symbol_dto |
The one current accepted symbol for a gene: e.g., wg, pax2a. |
| gene_synonym_dtos |
None |
| gene_synonyms |
Holds between a Gene and a synonym. |
| gene_systematic_name |
The one current systematic name for a gene: e.g., YHR084W, R09F10.2. |
| gene_systematic_name_dto |
The one current systematic name for a gene: e.g., YHR084W, R09F10.2. |
| gene_type |
SOTerm describing gene type |
| gene_type_curie |
Curie of SOTerm describing gene type |
| gene_types_secondary |
SOTerm describing alternate gene types |
| generated_by |
Holds between a material entity and an Agent that generated it: e.g., Thomas Blumenthal, Kornberg Laboratory. |
| generated_by_identifier |
Identifier for Reagent generated_by field. |
| generation_method_dto |
None |
| genes |
None |
| genetic_map_band |
Genetic map predicted chromosome location eg 10q12 |
| genetic_map_position_centimorgan |
Genetic map distance calculated along a chromosome in centiMorgans: e.g., 22.3366 cM. |
| genetic_map_position_centimorgan_error |
Error in calculated genetic map distance in centiMorgans: e.g., 0.045 cM. |
| genetic_map_position_radiation |
Radiation hybrid map predicted chromosome location: e.g., 66.5 cR. |
| genetic_sex |
Submitted value should be a vocabulary term from the 'Genetic sexes' vocabulary |
| genetic_sex_name |
Name of term from the 'Genetic sexes' vocabulary |
| genetically_interacts_with |
holds between two genes whose phenotypic effects are dependent on each other in some way - such that their combined phenotypic effects are the result of some interaction between the activity of their gene products. Examples include epistasis and synthetic lethality. |
| genome_assembly |
The GenomeAssembly to which a AssemblyComponent belongs. |
| genome_assembly_identifier |
The identifier for the GenomeAssembly. This can be a MOD curie, a MOD internal ID or an external (3rd party) identifier. |
| genome_assembly_ingest_set |
None |
| genomic_entity_identifier |
None |
| genomic_entity_relation_name |
Name of the VocabularyTerm describing the relationship between Construct and GenomicEntity |
| genomic_entity_type |
SOTerm describing genomic entity type |
| genomic_entity_type_curie |
Curie of SOTerm describing genomic entity type |
| genomic_information |
A collection of information that represents the strain or genomic background of the sample, either an id or free text |
| genomic_information_dto |
A collection of information that represents the strain or genomic background of the sample, either an id or free text |
| germline_transmission_status |
For alleles made in cell lines, have they been transmitted to the germline of an animal |
| germline_transmission_status_name |
Name of the VocabularyTerm representing the germline transmission status |
| go_term |
the Gene Ontology (GO) term to which the gene is being annotated |
| go_term_curie |
the Gene Ontology (GO) term to which the gene is being annotated |
| handle |
A slot pointing to a free-text alias or 'handle' for a data object, such as a reference-specific alias for a data object used while curating. |
| has_allele |
None |
| has_input |
None |
| has_output |
None |
| has_participant |
None |
| heading_term |
The MeSH term description or definition from PubMed. e.g. Measles in a Measles/epidemiology term. |
| heavy_chain_isotype |
The isotype of the antibody heavy chain: e.g., IgA. |
| heavy_chain_isotype_name |
Name of the VocabularyTerm representing the isotype of the antibody heavy chain: e.g., IgA. From the Heavy Chain Isotope CV. |
| height |
The height of the image (pixels). |
| hgvs |
HGVS nomenclature for variant located on a genomic entity. In practice HGVS nomenclature will be derived for any or all of VariantGenomicLocationAssociation, VariantTranscriptLocationAssociation, and VariantPolypeptideLocationAssociation. |
| hgvs_coding_nomenclature |
HGVSc nomenclature for variation in coding sequence |
| hgvs_protein_nomenclature |
HGVSp nomenclature for variation in protein |
| high_throughput_expression_dataset_annotation_ingest_set |
None |
| high_throughput_expression_dataset_sample_annotation_ingest_set |
None |
| homepage_resource_descriptor_page |
ResourceDescriptorPage containing URL template for organization's homepage |
| homology_confidence |
Confidence of homology match Permissible values: moderate / high / low |
| html_file_path |
File path of the HTML file generated from the BIRT report |
| htp_expression_dataset |
A identifier object for high throughput (HTP) expression dataset, as defined in htpId.json |
| htp_expression_dataset_dto |
A identifier object for high throughput (HTP) expression dataset, as defined in htpId.json |
| htp_expression_sample |
The IDs for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId |
| htp_expression_sample_age |
a collection of terms that when used together represent the age and stage of the sample |
| htp_expression_sample_age_dto |
a collection of terms that when used together represent the age and stage of the sample |
| htp_expression_sample_dto |
The IDs for this sample object, MOD or external database ID (ex: GEO); primaryId and secondaryId |
| htp_expression_sample_location_dtos |
A collection of terms that when used together represents the location within an organism from which the sample was taken |
| htp_expression_sample_locations |
A collection of terms that when used together represents the location within an organism from which the sample was taken |
| htp_expression_sample_title |
The free text title of the sample |
| htp_expression_sample_type |
Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below. |
| htp_expression_sample_type_curie |
Ontology ID of the biosample type. EX: total mRNA, OBI:XXXXXXX. See enumeration below. |
| id |
Precedence of identifiers for references is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. |
| id_example |
Example ID for the resource that fits the pattern described by the id_pattern slot |
| id_pattern |
Regex for the expected format of the ID |
| identity |
Identity score between the two genes |
| image_curie |
None |
| image_file |
The file representing the full-sized version of this image. |
| image_medium_file |
The file representing a medium-sized version of this image. |
| image_thumbnail_file |
The file representing the thumbnail of this image. |
| image_x_origin |
The x coordinate start point when specifying a spatial section within a larger image. |
| image_y_origin |
The y coordinate start point when specifying a spatial section within a larger image. |
| images |
Any associated image |
| in_collection |
Set of high-throughput alleles made by large projects |
| in_collection_name |
Name of VocabularyTerm describing the collection from the 'Allele collection vocabulary' Vocabulary |
| inchi |
InChi style description of the molecule |
| inchi_key |
InChi key description of the molecule |
| inferred_allele |
The allele to which something is inferred to be associated. |
| inferred_allele_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of allele to which something is inferred to be associated via an automated pipeline |
| inferred_gene |
The gene to which something is inferred to be associated. |
| inferred_gene_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of gene to which something is inferred to be associated via an automated pipeline |
| inheritance_mode |
Mode of inheritance, e.g. dominant / semi-dominant / recessive / unknown / codominant |
| inheritance_mode_name |
Name of VocabularyTerm describing the inheritance mode from the 'Allele inheritance mode vocabulary', e.g. dominant / semi-dominant / recessive / unknown / codominant |
| inserted_sequence |
The sequence of DNA base pairs inserted into the reference sequence by the variant. |
| integration_method |
WormBase captures the method by which an extrachromosomal transgene was integrated into the genome. |
| integration_method_name |
WormBase captures the method by which an extrachromosomal transgene was integrated into the genome. |
| interaction_id |
Identifier for interaction provided by MOD or other external source |
| interaction_source |
The interaction database that curated the interaction. e.g. BioGRID An MITerm from the AGR interaction source subset of AGR terms. |
| interaction_source_curie |
The interaction database that curated the interaction. e.g. BioGRID. Value is the curie of an MITerm from the AGR interaction source subset of AGR terms. |
| interaction_type |
The type of interaction between the two genes or gene products. e.g. physical association. An MITerm from the AGR interaction type subset of MITerms |
| interaction_type_curie |
The type of interaction between the two genes or gene products. e.g. physical association. Value is the curie of an MITerm from the AGR interaction type subset of MITerms |
| interactor_A_genetic_perturbation |
None |
| interactor_A_genetic_perturbation_curie |
None |
| interactor_A_role |
An MITerm from the AGR interactor A role subset of MITerms |
| interactor_A_role_curie |
Curie of an MITerm from the AGR interactor A role subset of MITerm |
| interactor_A_type |
An MITerm from the AGR interaction type subset of MITerms |
| interactor_A_type_curie |
Curie of an MITerm from the AGR interaction type subset of MITerms |
| interactor_B_genetic_perturbation |
None |
| interactor_B_genetic_perturbation_curie |
None |
| interactor_B_role |
An MITerm from the AGR interactor B role subset of MITerms |
| interactor_B_role_curie |
Curie of an MITerm from the AGR interactor B role subset of MITerms |
| interactor_B_type |
An MITerm from the AGR interaction type subset of MITerms |
| interactor_B_type_curie |
Curie of an MITerm from the AGR interaction type subset of MITerms |
| interacts_with |
holds between any two entities that directly or indirectly interact with each other |
| internal |
Classifies the entity as private (for internal use) or not (for public use). |
| intron_number |
The intron number of the variant location. If the variant is in an exon, this slot is not populated. Primarily used for zebrafish. |
| irradiation_mutagen |
The irradiation used to generate the mutation through mutagenesis |
| irradiation_mutagen_name |
The name of the irradiation used to generate the mutation through mutagenesis |
| is_best_reverse_score |
DIOPT schema highlights the best pair Permissible values: Yes / No |
| is_best_score |
DIOPT schema highlights the best pair Permissible values: Yes / No / Yes_Adjusted |
| is_extinct |
Does the allele still exist in a population somewhere? |
| is_extrachromosomal |
Used by WormBase to indicate whether a transgenic allele is known to be extrachromosomal. |
| is_integrated |
Used by WormBase to indicate whether a transgenic allele is known to be integrated into the genome. |
| iso_abbreviation |
|
| issue_name |
The number of the journal issue in which the article was published. From PubMed otherwise from Mod or manual reference creation. |
| iupac |
IUPAC name of the molecule |
| keywords |
Keywords tagging a publication. Aggregation of PubMed and ZFIN, editable at Alliance. |
| label |
A short display name for the figure. For example: Figure 2, Figure 3B |
| laboratory_of_origin |
The laboratory of origin for the entity. |
| laboratory_of_origin_curie |
The curie of the laboratory of origin for the entity. |
| language |
Language of the reference. Aggregation of PubMed and FlyBase, editable at Alliance. |
| last |
last identifier in a range |
| last_name |
last (family) name of a person |
| left_boundary_marker |
The left boundary of a feature location relative to the landmark's inherent orientation. |
| length |
The length of the aligned regions between two genes |
| light_chain_isotype |
The isotype of the antibody light chain: e.g., i4. |
| light_chain_isotype_name |
Name of the VocabularyTerm representing the isotype of the antibody light chain: e.g., i4. From the Light Chain Isotope CV. |
| linkml_schema_version |
Release of LinkML for which the file was generated and submitted |
| linkml_version |
Version of LinkML schema used for submitted file in the format n.n.n (e.g. 1.2.4 or 2.0.0) |
| load_exceptions |
A list of execeptions the load encountered |
| load_files |
None |
| load_finished |
The date and time that the load finished. |
| load_started |
The date and time that the load started. |
| loads |
None |
| local_file_path |
Local file path to where the file has been saved for processing |
| manufactured_by |
Holds between a material entity and an Agent that has manufactured it: e.g., Molecular Probes. |
| manufactured_by_identifier |
Identifier for Reagent manufactured_by field. |
| maps_to_chromosome |
The chromosome(s) to which a chromosome assembly or unlocalized scaffold or contig maps. |
| md5_sum |
Generated md5Sum of the file that has been uploaded |
| medline_abbreviation |
|
| member_terms |
Set of VocabularyTerm objects in a Vocabulary object set |
| merged_into |
For an entity deprecated by a merge, the entity into which it was merged. |
| merged_into_id |
ID that used to refer to this reference |
| mesh_detail_id |
The primary key for a MeshDetail object. |
| microarray_sample_details |
collection of information that is specific for microarray samples |
| microarray_sample_details_dto |
collection of information that is specific for microarray samples |
| middle_name |
middle names of a person |
| mod_corpus_association_id |
An integer referring to a ModCorpusAssociation object. A primary key in the mod_corpus_association table, a foreign key if used in other tables. |
| mod_corpus_sort_source |
origin of corpus determination for that publication and mod |
| mod_internal_id |
The model organism database (MOD) internal identifier for the object |
| moderate_filter |
Indicates whether this homology match is displayed when the moderate filter is selected |
| mutagenesis_method_names |
Name of the VocabularyTerm describing the mutagenesis method, e.g. spontaneous / naturally occurring / radiation-induced / recombinant / ENU / CRISPR / TALEN / gamma rays / not specified / spontaneous / DNA / DNA AND CRISPR / DNA and TALEN / zinc finger nuclease / EMS |
| mutagenesis_methods |
Technique used to create the allele, e.g. spontaneous / naturally occurring / radiation-induced / recombinant / ENU / CRISPR / TALEN / gamma rays / not specified / spontaneous / DNA / DNA AND CRISPR / DNA and TALEN / zinc finger nuclease / EMS |
| mutagenesis_target |
The target of the mutation, e.g. strain / adult females / adult males / embryos / sperm / not specified |
| mutation_target_strain |
The particular strain (solely for and from MGI) that is targeted by the generation method for a particular allele. |
| mutation_target_strain_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the particular strain that is targeted by the generation method for a particular allele (MGI only) |
| mutation_type_curies |
Curies of SOTerms representing mutation type |
| mutation_types |
SO term for type of mutation |
| name |
a human-readable name for an entity |
| name_type |
The type of name: e.g., symbol, full_name, systematic_name, etc. |
| name_type_name |
Name of the VocabularyTerm representing the name type of the synonym - proposed values are nomenclature_symbol / full_name / systematic_name / ncbi_protein_name / uniform / non_uniform / retired_name / unspecified |
| namespace |
the namespace of the ontology. |
| negated |
if set to true, then the association is negated i.e. is not true |
| nomenclature_event |
any of the kinds of changes made to an object's name or symbol |
| nomenclature_event_name |
Name of the VocabularyTerm describing the nomenclature event |
| note_dto |
None |
| note_dtos |
None |
| note_type |
The type of note: e.g., cytology, comment, summary. |
| note_type_name |
Name of VocabularyTerm representing note type selected from the appropriate Vocabulary |
| number_additional_dna_base_pairs |
The number of additional DNA base pairs inserted into the reference sequence by the variant. |
| number_amino_acids_inserted |
The number of amino acids added from the polypeptide as a result of the variant. |
| number_amino_acids_removed |
The number of amino acids removed from the polypeptide as a result of the variant. |
| number_of_channels |
For microarrays, the number of channels used; This can be one of two values: 1 or 2 |
| number_removed_dna_base_pairs |
The number of DNA base pairs removed from the reference sequence by the variant. sequence. |
| object_allele_identifier |
The identifier (curie/primary_external_id/mod_internal_id) of the allele that is acting as the object of an AlleleAlleleAssociation |
| object_gene |
The second gene in the homology match pair |
| object_gene_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the object gene in a gene-to-gene association |
| object_set |
Applies to a property that links a ingest object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types |
| obsolete |
Entity is no longer current. |
| okta_email |
The email address of the LoggedInPerson registered with Okta for user authentication |
| okta_id |
The Okta identifier for the person registered in Okta for user authentication |
| old_emails |
list of old (outdated) emails for a person |
| old_members |
Gene which were formerly members of this GeneClass |
| online_issn |
|
| ontology_closure_ingest_set |
None |
| ontology_term_closure_object |
None |
| ontology_term_closure_subject |
None |
| ontology_type |
None |
| open_access |
Indicates if the reference is freely available for use by anyone, usually with fewer copyright and licensing barriers. |
| orcid |
Open Researcher and Contributor ID |
| original_reference |
Holds between an entity and the first reference to describe that entity. |
| original_reference_curie |
Curie of the first reference to describe an entity. |
| padded_base |
A base preceded an insertion or deletion event that is reported when either the reference or variant sequence would otherwise be empty. |
| page_area |
None |
| page_description |
Description of page |
| page_range |
Page numbers of source referenced for statement or publication. From PubMed otherwise from Mod or manual reference creation. |
| paralogous_genes |
None |
| parental_populations |
None |
| pdf_file_path |
File path of the PDF file generated from the BIRT report |
| phase |
Number of nucleotides from the start of a feature to the start of a complete codon |
| phenotype_agm_ingest_set |
None |
| phenotype_allele_ingest_set |
None |
| phenotype_annotation_object |
phenotype statement: The label of an individual phenotype term from a phenotype ontology or the post-composed statement of the phenotype from a post-composed terminology |
| phenotype_annotation_subject |
The biological entity (e.g. gene, allele, genotype) to which the phenotype is associated, by direct curation. |
| phenotype_gene_ingest_set |
None |
| phenotype_statement |
For MODs that curate to post-composed phenotype expressions composed of ontology terms and other necessary information (e.g. vocabularies, free text). This field captures the free text phenotype statement. |
| phenotype_term |
The phenotype ontology term used to describe the phenotype of an organism or a set of organisms. |
| phenotype_term_curie |
The string representation of the phenotype ontology term (PhenotypeTerm) curie |
| phenotype_term_curies |
The string representation of the phenotype ontology term (PhenotypeTerm) curie |
| phenotype_terms |
The phenotype ontology term used to describe the phenotype of an organism or a set of organisms. |
| phenotypes_or_traits |
None |
| phylogenetic_order |
The integer value assigned to a species to determine its relative ordering with respect to other Alliance species in various user interface displays and logical operations. |
| physically_interacts_with |
holds between two entities that make physical contact as part of some interaction |
| plain_language_abstract |
Lay person, readable version of the abstract. Only relevant for PubMed references. |
| polyphen_prediction |
PolyPhen-2 prediction |
| polyphen_score |
PolyPhen-2 score between 0 and 1 |
| predicted_variant_consequences |
VEP-calculated variant consequences |
| prediction_methods_matched |
Source of the homology match |
| prediction_methods_not_called |
Prediction methods that were not called |
| prediction_methods_not_matched |
Prediction methods not matched |
| preferred_cross_reference |
cross reference to the preferred page to link to in search |
| preferred_cross_reference_dto |
cross reference to the preferred page to link to in search |
| prefix |
Denormalization to help with classifying types of crossReferences, distinguishing DOIs from PMC ids, etc. |
| prefix_order |
The relative order of the resource when listed with other crossReferences. |
| prefix_page |
The category of pages the resource in the context of the URL associated with the crossReference provides. Equivalent to the 'page' attribute in the Alliance resourceDescriptor file. |
| primary_external_id |
The primary external (non-Alliance) database identifier/curie for the object. Note that this may be an external (non-Alliance member) identifier for an object, like a UniProt ID for a protein, and may act as the MOD's/Alliance member's primary key for the entity. |
| primary_image |
The primary image for an allele that is used to represent the allele on a page. |
| print_issn |
|
| product_binds_matrix |
WB specific. ID of position matrix object |
| protein_identifier |
None |
| protein_ingest_set |
None |
| proteins |
None |
| publisher |
Publisher associated with a reference or resource. From PubMed otherwise from Mod or manual reference creation. |
| pubmed_abstract_languages |
Languages for the abstract. Only relevant for PubMed references. |
| pubmed_publication_status |
Status of the publication at PubMed. Only relevant for PubMed references. |
| pubmed_type |
Type of Reference as described by PubMed. Only relevant for PubMed references. |
| qualifier_term |
The MeSH term subheading from PubMed, to narrow down the topic. e.g. epidemiology in a Measles/epidemiology term. |
| qualifiers |
This is the MeSH qualifier term that is optionally added to the descriptor term. |
| rank |
The rank (order) of the paralog result |
| record_count |
The number of records found in the file |
| reference_curie |
External reference curie used for ingest |
| reference_curies |
External reference curies used for ingest |
| reference_id |
An integer referring to a Reference object in the references table. It's a primary key in the references table, a foreign key when in other tables. |
| reference_sequence |
Reference sequence of genome or genomic entity at position of aligned variant. |
| referenced_curie |
Curie of the thing being referenced in a CrossReference |
| references |
holds between an object and a list of references |
| related_figure |
Holds between an entity and a single Figure. Singular version of related_figures. |
| related_figures |
Holds between an entity and a set of Figures. |
| related_note |
Holds between an object and a Note object. |
| related_notes |
Holds between an object and a list of related Note objects. |
| related_to |
A relationship that is asserted between two named things. |
| relation |
A high-level grouping for the relationship type. This is analogous to category for nodes. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. |
| relation_name |
Name of VocabularyTerm representing relation of an Association |
| relationship_type |
None |
| release |
MOD release ID |
| resource_descriptor_page |
None |
| resource_id |
None |
| resource_pages |
Pages for a particular resource |
| right_boundary_marker |
The right boundary of a feature location relative to the landmark's inherent orientation. |
| s3_path |
The relative path to the file in the S3 bucket |
| s3_url |
The full URL to the file from S3 |
| schedule_active |
This determines if the the schedule is active or not |
| scheduling_error_message |
Error message for scheduling of curation reports |
| secondary_data_provider |
Object representing organization (e.g. MOD) that provided the data directly to the Alliance, but not the original source |
| secondary_data_provider_cross_reference |
CrossReference to the organization that provided the data to the Alliance |
| secondary_data_provider_dto |
Ingest object representing organization (e.g. MOD) that provided the data directly to the Alliance, but not the original source, and a CrossReference to that organisation's site |
| secondary_id |
None |
| secondary_identifiers |
None |
| sequence_targeting_reagent_association_subject |
None |
| sequence_targeting_reagent_gene_association_object |
None |
| sequence_targeting_reagent_gene_associations |
None |
| sequence_targeting_reagent_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the STR |
| sequence_targeting_reagent_identifiers |
Identifiers (curie/primary_external_id/mod_internal_id) of the STRs |
| sequence_targeting_reagents |
None |
| sequencing_format |
single or paired end sequencing; might be better in experiment info |
| sgd_strain_background |
None |
| sgd_strain_background_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of SGD strain background AGM |
| short_name |
The short name of the entity |
| sift_prediction |
SIFT prediction |
| sift_score |
SIFT score between 0 and 1 |
| similarity |
Similarity score between the two genes |
| single_agm |
None |
| single_allele |
None |
| single_construct |
None |
| single_gene |
None |
| single_reference |
holds between an object and a single reference |
| single_variant |
The variant that is the subject of a SlotAnnotation. |
| smiles |
Molecular structure in SMILES format |
| source_general_consequence_curie |
Curie of the SOTerm (child of SO:0001576 - transcript_variant) that describes the consequence of the variant, as stated in the source reference when no transcript ID is provided. Since a curator would determine variant location and consequences relative to at least one specific genome assembly, transcript and/or polypeptide, no slot for curated general consequence is provided. |
| source_general_consequence_dtos |
None |
| source_general_consequences |
None |
| source_organization_abbreviation |
None |
| source_variant_genomic_location_association_ingest_set |
None |
| source_variant_genomic_locations |
Location of the variant in a genomic context as described by the source reference. Multivalued as there may be multiple source references. |
| source_variant_polypeptide_locations |
Location of the variant within polypeptide entities as described by the source reference. |
| source_variant_protein_location_association_ingest_set |
None |
| source_variant_transcript_location_association_ingest_set |
None |
| source_variant_transcript_locations |
Location of the variant within transcript entities as described by the source reference. |
| specimen_alleles |
The Allele(s) of the specimen assayed. |
| specimen_genomic_model |
The AffectedGenomicModel of the specimen. |
| specimen_genomic_model_identifier |
The identifier of the AffectedGenomicModel of the specimen. This can be a MOD curie, a MOD internal ID or an external (3rd party) identifier. |
| split_from |
For an entity generated by a split, the entity from which it was split. |
| split_into |
For an entity deprecated by a split, the list of entities generated from the split. |
| sqtr_gene_association_ingest_set |
None |
| sqtr_ingest_set |
None |
| stage |
The life stage of an organism or biosample as expressed by a TemporalContext entity |
| stage_dto |
The life stage of an organism or biosample as expressed by a TemporalContext entity |
| stage_uberon_slim_term_curies |
The high-level UBERON slim terms that apply to the developmental range of the TemporalContext component of an ExpressionPattern. The following UBERON terms are allowed: UBERON:0000068, UBERON:0000113. A non-UBERON term is also allowed: post embryonic, pre-adult. |
| stage_uberon_slim_terms |
The high-level UBERON slim terms that apply to the developmental range of the TemporalContext component of an ExpressionPattern. The following UBERON terms are allowed: UBERON:0000068, UBERON:0000113. A non-UBERON term is also allowed: post embryonic, pre-adult. |
| start |
The start of the feature in positive 1-based integer coordinates relative to the reference landmark. |
| strand |
The strand of a DNA reference object to which an entity maps. |
| strict_filter |
Indicates whether this homology match is displayed when the strict filter is selected |
| sub_series |
If the dataset is a SuperSeries, this is a list of dataset ids that are associated with this dataset |
| subdomain_code |
a three letter string, representing a subdomain (e.g 101 represents disease_annotation) |
| subdomain_name |
subdomain name (e.g disease_annotation) |
| subject_gene |
The first gene in the homology match pair |
| subject_gene_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the subject gene in a gene-to-gene association |
| subsets |
None |
| subtype |
Subtype of affected genomic model - permissible values: strain / genotype / fish |
| subtype_name |
Name of VocabularyTerm describing subtype - permissible values: strain / genotype / fish |
| summary |
|
| symbol_renamed_from |
The previous symbol for a renamed entity. |
| symbol_renamed_to |
The new symbol for a renamed entity. |
| synonym_scope |
the scope of the synonym - permissible values are narrow / broad / related / exact |
| synonym_scope_name |
Name of the VocabularyTerm representing the scope of the synonym - permissible values are narrow / broad / related / exact |
| synonym_url |
URL for a synonym: e.g., NCBI URL for the NCBI synonym of an object. |
| synonyms |
A generic free-text field for objects that only have string representation of one or more synonyms and do not require meta data or attribution; if meta data or attribution are required to be captured for individual synonyms, consider the NameSlotAnnotation class |
| table_key |
The primary key for a specific table entry, unique for that table. |
| taxon |
The taxon from which the biological entity derives. |
| taxon_curie |
Curie of the NCBITaxonTerm representing the taxon from which the biological entity derives |
| taxon_text |
The free text reference to a species or general taxon (e.g. "Yeast") for a a biological entity for which the exact taxon curie is unknown or unavailable. |
| temporal_qualifier_names |
Qualifiers of the stage or age in an annotation. The range is a string representing vocabulary term |
| temporal_qualifiers |
Qualifiers of the stage or age in an annotation. |
| title |
A human readable title for a reference. From PubMed otherwise from Mod or manual reference creation. |
| total_records |
The total number of records |
| trans_splice_leaders |
Trans-splicing splice leaders observed to operate on this gene, in species which have spliced leader trans-splicing |
| transcript_association_subject |
Subject slot to be used for transcript associations |
| transcript_cds_associations |
None |
| transcript_coding_sequence_association_object |
None |
| transcript_exon_association_object |
None |
| transcript_exon_associations |
None |
| transcript_gene_association |
None |
| transcript_gene_association_object |
None |
| transcript_genomic_location_association_object |
None |
| transcript_genomic_location_associations |
None |
| transcript_id |
The transcript identifier used by the Ensembl VEP to identify the transcript and generate HGVSc identifiers. This corresponds to the transcript_id attribute in column 9 of transcript entries in the GFF files. |
| transcript_identifier |
None |
| transcript_ingest_set |
None |
| transcript_type |
SOTerm describing transcript type |
| transcript_type_curie |
Curie of SOTerm describing transcript type |
| transgene_chromosome_location |
The chromosome to which a transgene has been mapped. Used for WormBase transgenes that have been integrated into the genome and mapped to a chromosome. |
| transgene_chromosome_location_name |
The name of the chromosome to which a transgene has been mapped. Used for WormBase transgenes that have been integrated into the genome and mapped to a chromosome. |
| transposon_insertion |
Associated transposon insertion that causes the mutation |
| transposon_origin |
If this gene contains or is originating from a transposon |
| type |
None |
| uncertain |
If set to true, then the related entity is uncertain. |
| unique_id |
A non-curie unique identifier for a thing. |
| updated_by |
The individual that last modified the entity. |
| updated_by_curie |
Curie of the Person object representing the individual that updated the entity |
| url_prefix |
The prefix of the url before the accession number. |
| url_suffix |
The suffix of the url after the accession number. |
| url_template |
URL template for constructing link to resource using provided ID, eg. "https://www.omim.org/phenotypicSeries/[%s]" |
| user_settings |
JSON Blob containing details of UI settings for LoggedInPerson |
| variant_association_subject |
Subject slot to be used for variant associations |
| variant_genomic_location |
VariantGenomicLocationAssociation for which consequences are calculated |
| variant_genomic_location_association_ingest_set |
None |
| variant_genomic_location_association_object |
The location reference object should be a chromosome assembly curie. |
| variant_identifier |
Identifier (curie/primary_external_id/mod_internal_id) of the variant |
| variant_ingest_set |
None |
| variant_locations |
Location of the variant within genomic entities. Variant_locations can include any or all of: one VariantGenomicLocationAssociation stanza, one or more VariantTranscriptLocationAssociation stanzas and/or one or more VariantPolypeptideLocationAssociation stanzas. |
| variant_polypeptide_location_association_object |
Polypeptide associated with variant and for which a specific location and consequence of that variant is provided, as specified by curator. Multivalued=false for this slot because although a variant can have multiple VariantPolypeptideLocationAssociation stanzas, each stanza will have one and only one curated polypeptide ID. |
| variant_protein_location_association_ingest_set |
None |
| variant_sequence |
Sequence that differs from the reference sequence of genome or genomic entity at position of variant, as specified by curator. |
| variant_source_general_consequence |
The general consequence of the variant on the transcript. |
| variant_status |
VocabularyTerm describing the status of the variant. From the Variant Status CV |
| variant_status_name |
Name of the VocabularyTerm describing the status of the variant. From the Variant Status CV |
| variant_transcript |
Transcript to which variant effect prediction applies |
| variant_transcript_location_association_ingest_set |
None |
| variant_transcript_location_object |
Transcript associated with variant and for which a specific location and consequence of that variant is provided, as specified at source. Multivalued=false for this slot because although a variant can have multiple VariantTranscriptLocationAssociation stanzas, each stanza will have one and only one source transcript ID. |
| variant_type |
SOTerm describing the type of variant. In practice, variant type will be limited to a subset of the SO specified in an Alliance controlled vocabulary in order to maintain consistency. |
| variant_type_curie |
Curie of the SOTerm describing the type of variant. In practice, variant type will be limited to a subset of the SO specified in an Alliance controlled vocabulary in order to maintain consistency. |
| variation_strand |
The strand on which the variant is located. This is the strand of the reference sequence, not the variant sequence. |
| vep_consequences |
VEP consequence |
| vep_impact |
VEP predicted impact of variation on molecule |
| video_still |
An image represents a video still. |
| vocabulary_description |
The free text description of a Vocabulary including its intended use. |
| vocabulary_label |
Immutable label used for identification of vocabulary or vocabulary term set. This is distinct from the "name" slot in that it cannot be changed once created. |
| vocabulary_term_set_description |
The free text description of a VocabularyTermSet including its intended use. |
| vocabulary_term_set_vocabulary |
The Vocabulary from which the terms contained in theVocabularyTermSet belong |
| volume |
Volume associated with a reference. From PubMed otherwise from Mod or manual reference creation. |
| wbprocess |
WB specific. Eg WBbiop00000015 Corpse engulfment |
| when_expressed |
When some entity is observed to be present in a specimen. If no temporal information is available for an annotation, use a root stage term for the developmental_stage_start. |
| when_expressed_stage_name |
A human-readable stage name. To be used when an ontology term for the relevant stage is not available. |
| where_expressed |
Where some entity is observed to be present in a specimen. If no spatial information is available for an annotation, use a root anatomical term for the anatomical_structure. |
| where_expressed_statement |
A human-readable free-text description of the anatomical location of the expression pattern. |
| width |
The width of the image (pixels). |
| with_gene_identifiers |
Identifier (curie/primary_external_id/mod_internal_id) of genes http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8 |
| with_or_from |
http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/#with-or-from-column-8 |
| xls_file_path |
File path of the Excel file generated from the BIRT report |
| zygosity |
GENO ontology ID for allele zygosity |
| zygosity_curie |
Curie of GENO ontology ID for allele zygosity - permissible_values: GENO:0000602 / GENO:0000603 / GENO:0000604 / GENO:0000605 / GENO:0000606 / GENO:0000135 / GENO:0000136 / GENO:0000137 / GENO:0000134 |