ZFIN Data Reports from: 20 Apr 2018

 Warranty Disclaimer and Copyright Notice  
ZFIN data reports are updated every day of the week at 10:10pm PST with the exception of the externally hosted files. The format for each file is described below. All files use tab as the field delimiter. The 'Download File' link will display the file in your browser. Click the download button to save the file onto your local system (includes timestamp and header info). If you choose to link to a ZFIN data page from your web site, append the ZFIN ID to the URL http://zfin.org/
e.g. http://zfin.org/ZDB-GENE-980526-166
for the 'shha' gene. Please direct questions or requests for additional data to ZFIN.
View Archive Files
Category Download File Download
w Header		 Column Headers File Size Number of Records
Anatomical Ontologies Zebrafish Anatomy Term
Show 213 KB 3,018
1 2 3 4
Anatomy ID Anatomy Name Start Stage ID End Stage ID
Zebrafish Anatomy Term Relationships
Show 175 KB 5,815
1 2 3
Parent Item ID Child Item ID Relationship Type ID
Zebrafish Anatomy Term Relationships
Show 175 KB 5,815
1 2 3
Parent Item ID Child Item ID Relationship Type ID
Zebrafish Anatomy Term Synonyms
Show 149 KB 2,867
1 2 3
Anatomy OBO ID Anatomy Name Anatomy Synonym
Zebrafish Anatomy Term Synonyms
Show 149 KB 2,867
1 2 3
Anatomy OBO ID Anatomy Name Anatomy Synonym
Zebrafish Development Stage Terms
Show 315 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 315 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 315 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Antibody Data Antibody Expressions in wild-type
Show 411 KB 7,466
1 2 3 4 5
Antibody ID AnatomyStructure ID AnatomyStructure Name Substructure ID Substructure Name
Antibody Expressions in wild-type
Show 411 KB 7,466
1 2 3 4 5
Antibody ID AnatomyStructure ID AnatomyStructure Name Substructure ID Substructure Name
Fish Data Experiment Details
Show 16 MB 1,008,955
1 2 3 4 5 6
Experiment ID ZECO Term ID ZFA Term ID GO Cellular Component Term ID Chebi Term ID NCBI Taxon Term ID
Fish Components
Show 8 MB 54,566
1 2 3 4 5 6 7 8 9 10 11 12
Fish ID Fish Name Gene ID Gene Symbol Affector ID Affector Symbol Construct ID Construct Symbol Background ID Background Name Genotype ID Genotype Name
Fish Components
Show 8 MB 54,566
1 2 3 4 5 6 7 8 9 10 11 12
Fish ID Fish Name Gene ID Gene Symbol Affector ID Affector Symbol Construct ID Construct Symbol Background ID Background Name Genotype ID Genotype Name
Genotype Backgrounds
Show 522 KB 8,049
1 2 3 4
Genotype ID Genotype Name Background Background Name
Genotype Features
Show 5 MB 30,482
1 2 3 4 5 6 7 8 9 10 11 12 13
Genotype ID Genotype Name Genotye Unique Name Allele ID Allele Name Allele Abbreviation Allele Type Allele Display Type Gene or Construct Symbol Corresponding ZFIN Gene ID/Construct ID Allele Zygosity Construct Name Construct ZdbId
Genotype Features
Show 5 MB 30,482
1 2 3 4 5 6 7 8 9 10 11 12 13
Genotype ID Genotype Name Genotye Unique Name Allele ID Allele Name Allele Abbreviation Allele Type Allele Display Type Gene or Construct Symbol Corresponding ZFIN Gene ID/Construct ID Allele Zygosity Construct Name Construct ZdbId
Genotype Features (removed or displaced genes)
Show 32 KB 320
1 2 3 4 5
Genotype ID Genotype Name Genotye Unique Name Affected Genomic Region Symbol Corresponding ZFIN Gene ID
Gene Expression Expression data for wildtype fish
Show 31 MB 195,306
1 2 3 4 5 6 7 8 9 10 11 12 13 14
Gene ID Gene Symbol Fish Name Super Structure ID Super Structure Name Sub Structure ID Sub Structure Name Start Stage End Stage Assay Publication ID Probe ID Antibody ID Fish ID
Expression Environment Description
Show 715 KB 10,717
1 2 3 4 5 6 7 8 9 10 11
Environment ID ZECO Term Name ZECO Term ID (ZECO:ID) Chebi Term Name Chebi Term ID (Chebi:ID) ZFA Term Name ZFA Term ID (ZFA:ID) Affected Structure Subterm Name Affected Structure Subterm ID (GO-CC:ID) NCBI Taxon Name NCBI Taxon ID (NCBI Taxon:ID)
Expression Experiment-Figure
Show 16 MB 360,120
1 2 3
Expression ID Expression Result ID Figure ID
Zebrafish Gene Expression by Stage and Anatomy Term
Show 32 MB 596,627
1 2 3 4 5 6 7
Expression Result ID Expression ID Start Stage ID End Stage ID Anatomy Super Term ID Anatomy Sub Term ID Expression Found
Zebrafish Gene Expression by Stage and Anatomy Term
Show 32 MB 596,627
1 2 3 4 5 6 7
Expression Result ID Expression ID Start Stage ID End Stage ID Anatomy Super Term ID Anatomy Sub Term ID Expression Found
ZFIN Genes with Expression Assay Records
Show 14 MB 113,242
1 2 3 4 5 6 7 8 9 10
Gene ID Gene Symbol EST ID (Optional) EST Symbol (Optional) Expression Type Expression ID Publication ID Fish ID Environment ID Probe Quality (optional 0 - 5 rating)
Genetic Marker Relationships Genetic Marker Relationships
Show 11 MB 109,872
1 2 3 4 5 6 7
Gene ID Gene SO ID Gene Symbol Marker ID Marker SO ID Marker Symbol Relationship
Genetic Marker Relationships
Show 11 MB 109,872
1 2 3 4 5 6 7
Gene ID Gene SO ID Gene Symbol Marker ID Marker SO ID Marker Symbol Relationship
Genetic Markers Genetic Marker
Show 10 MB 164,647
1 2 3 4 5
Marker ID Marker Symbol Marker Name Marker Type SO ID
Genetic Marker
Show 10 MB 164,647
1 2 3 4 5
Marker ID Marker Symbol Marker Name Marker Type SO ID
Previous ZFIN IDs
(includes former and current ZFIN IDs for merged data)
Show 1 MB 34,200
1 2
Former ZFIN ID Current ZFIN ID
Previous ZFIN IDs
(includes former and current ZFIN IDs for merged data)
Show 1 MB 34,200
1 2
Former ZFIN ID Current ZFIN ID
SNP Data
Show 149 MB 2,674,896
1 2 3 4
Marker ID Marker Symbol SNP rs accession number Publication ZDB ID
Genomic Feature Data All Genomic Features
Show 6 MB 64,878
1 2 3 4 5 6 7 8 9 10 11 12
Genomic Feature ID Feature SO ID Genomic Feature Abbreviation Genomic Feature Name Genomic Feature Type Mutagen Mutagee Construct ID Construct name Construct SO ID TALEN/CRISPR ID TALEN/CRISPR Name
Construct Components
Show 1 MB 9,993
1 2 3 4 5 6 7 8 9
Construct ID Construct Name Construct Type Component ID Component Name Component Type Relationship Construct SO ID Component SO ID
Transgenic Insertions
Show 3 MB 29,954
1 2 3 4 5 6 7
Genomic Feature ID Genomic Feature Abbreviation Genomic Feature Name Feature SO ID Construct ID Construct Name Construct SO ID
Transgenic Insertions
Show 3 MB 29,954
1 2 3 4 5 6 7
Genomic Feature ID Genomic Feature Abbreviation Genomic Feature Name Feature SO ID Construct ID Construct Name Construct SO ID
Transgenic Insertions
Show 3 MB 29,954
1 2 3 4 5 6 7
Genomic Feature ID Genomic Feature Abbreviation Genomic Feature Name Feature SO ID Construct ID Construct Name Construct SO ID
Human Disease Gene to Disease via Orthology
Show 950 KB 7,074
1 2 3 4 5 6 7 8 9 10
Zebrafish Gene ID Zebrafish Gene Symbol Human Ortholog Entrez Gene Id Human Ortholog Symbol DO Term Name DO Term ID OMIM Term Name OMIM ID Evidence Code Publication
Gene to Disease via Orthology
Show 950 KB 7,074
1 2 3 4 5 6 7 8 9 10
Zebrafish Gene ID Zebrafish Gene Symbol Human Ortholog Entrez Gene Id Human Ortholog Symbol DO Term Name DO Term ID OMIM Term Name OMIM ID Evidence Code Publication
Human Disease/Models
Show 115 KB 929
1 2 3 4 5 6 7 8
Fish ZDB ID Environment ZDB ID is_a_model DO Term ID DO Term Name Publication ZDB ID PubMed ID Evidence Code
Image Data Image-Figure translations
Note: Images are not provided due to copyright restrictions
Show 5 MB 106,847
1 2 3
Image ID Figure ID Image Preparation
Image-Figure translations
Note: Images are not provided due to copyright restrictions
Show 5 MB 106,847
1 2 3
Image ID Figure ID Image Preparation
Image-Figure translations
Note: Images are not provided due to copyright restrictions
Show 5 MB 106,847
1 2 3
Image ID Figure ID Image Preparation
Knockdown Reagent Data CRISPR
Show 379 KB 2,900
1 2 3 4 5 6 7 8 9
Gene ID Gene SO ID Gene Symbol CRISPR ID CRISPR SO ID CRISPR Symbol CRISPR Target Sequence Publication(s) Note
Morpholino
Show 1 MB 9,462
1 2 3 4 5 6 7 8 9
Gene ID Gene SO ID Gene Symbol Morpholino ID Morpholino SO ID Morpholino Symbol Morpholino Sequence Publication(s) Note
Morpholino
Show 1 MB 9,462
1 2 3 4 5 6 7 8 9
Gene ID Gene SO ID Gene Symbol Morpholino ID Morpholino SO ID Morpholino Symbol Morpholino Sequence Publication(s) Note
Mapping Data Mapping Data from the 6 Zebrafish Mapping Panels
Show 1 MB 36,500
1 2 3 4 5 6
ZFIN ID Symbol Panel Symbol Chromosome Location Metric
Mapping Data from the 6 Zebrafish Mapping Panels
Show 1 MB 36,500
1 2 3 4 5 6
ZFIN ID Symbol Panel Symbol Chromosome Location Metric
Orthology Data Drosophila and Zebrafish Orthology
Show 8 KB 73
1 2 3 4 5 6 7 8 9
ZFIN ID ZFIN Symbol ZFIN Name Fly Symbol Fly Name Flybase ID Gene ID Evidence Pub ID
Drosophila and Zebrafish Orthology
Show 8 KB 73
1 2 3 4 5 6 7 8 9
ZFIN ID ZFIN Symbol ZFIN Name Fly Symbol Fly Name Flybase ID Gene ID Evidence Pub ID
Human and Zebrafish Orthology
Show 5 MB 38,796
1 2 3 4 5 6 7 8 9 10
ZFIN ID ZFIN Symbol ZFIN Name Human Symbol Human Name OMIM ID Gene ID HGNC ID Evidence Pub ID
Mouse and Zebrafish Orthology
Show 3 MB 28,272
1 2 3 4 5 6 7 8 9
ZFIN ID ZFIN Symbol ZFIN Name Mouse Symbol Mouse Name MGI ID Gene ID Evidence Pub ID
Phenotypic Zebrafish genes with Human Orthology
Show 142 KB 3,381
1 2 3 4 5
ZFIN ID ZFIN Symbol Entrez Zebrafish Gene ID Human Gene Symbol Entrez Human Gene ID
Phenotype Data Antibody Labeling Phenotypes
Show 394 KB 1,269
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Antibody Name Antibody ID SO Term SO ID RO Term RO ID Superstructure Name Superstructure ID Substructure Name Substructure ID Phenotype Keyword Name Phenotype Keyword ID Phenotype Tag Start Stage Name Start Stage ID End Stage Name End Stage ID Assay Fish ID Environment ID Figure ID Publication ID PubMed ID
Fish with Phenotypes
Show 29 MB 129,040
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Fish ID Fish Name Start Stage ID Start Stage Name End Stage ID End Stage Name Affected Structure or Process 1 subterm ID Affected Structure or Process 1 subterm Name Post-composed Relationship ID Post-composed Relationship Name Affected Structure or Process 1 superterm ID Affected Structure or Process 1 superterm Name Phenotype Keyword ID Phenotype Keyword Name Phenotype Tag Affected Structure or Process 2 subterm ID Affected Structure or Process 2 subterm name Post-composed Relationship (rel) ID Post-composed Relationship (rel) Name Affected Structure or Process 2 superterm ID Affected Structure or Process 2 superterm name Publication ID Environment ID
Fish with Phenotypes
Show 29 MB 129,040
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Fish ID Fish Name Start Stage ID Start Stage Name End Stage ID End Stage Name Affected Structure or Process 1 subterm ID Affected Structure or Process 1 subterm Name Post-composed Relationship ID Post-composed Relationship Name Affected Structure or Process 1 superterm ID Affected Structure or Process 1 superterm Name Phenotype Keyword ID Phenotype Keyword Name Phenotype Tag Affected Structure or Process 2 subterm ID Affected Structure or Process 2 subterm name Post-composed Relationship (rel) ID Post-composed Relationship (rel) Name Affected Structure or Process 2 superterm ID Affected Structure or Process 2 superterm name Publication ID Environment ID
Fish-Figure relation
Show 1 MB 43,033
1 2
Fish ID Figure ID
Fish-Figure relation
Show 1 MB 43,033
1 2
Fish ID Figure ID
Fish-Figure relation
Show 1 MB 43,033
1 2
Fish ID Figure ID
Phenotype Environment Description
Show 786 KB 11,992
1 2 3 4 5 6 7 8 9 10 11
Environment ID ZECO Term Name ZECO Term ID (ZECO:ID) Chebi Term Name Chebi Term ID (Chebi:ID) ZFA Term Name ZFA Term ID (ZFA:ID) Affected Structure Subterm Name Affected Structure Subterm ID (GO-CC:ID) NCBI Taxon Name NCBI Taxon ID (NCBI Taxon:ID)
Phenotype for Zebrafish genes with Human Orthology
Show 5 MB 44,048
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
Gene ID Entrez Zebrafish Gene ID Entrez Human Gene ID ZFIN Gene Symbol Affected Structure or Process 1 subterm OBO ID Affected Structure or Process 1 subterm name Post-Composed Relationship ID Post-Composed Relationship Name Affected Structure or Process 1 superterm OBO ID Affected Structure or Process 1 superterm name Phenotype Keyword OBO ID Phenotype Quality Phenotype Tag Affected Structure or Process 2 subterm OBO ID Affected Structure or Process 2 subterm name Post-Composed Relationship ID Post-Composed Relationship Name Affected Structure or Process 2 superterm OBO ID Affected Structure or Process 2 superterm name
Publications ZFIN Bibliography
Show 6 MB 25,880
1 2 3 4 5 6 7 8
Publication ID pubMed ID (none or blank when not available) Authors Title Journal Year Volume Pages
ZFIN Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs
Show 6 MB 97,998
1 2 3 4 5
ZFIN Marker ID SO ID UniProtKB ID PubMed ID ZFIN Annotation (GO/Phenotype/Expression)
ZFIN Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs
Show 6 MB 97,998
1 2 3 4 5
ZFIN Marker ID SO ID UniProtKB ID PubMed ID ZFIN Annotation (GO/Phenotype/Expression)
ZFIN Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs
Show 6 MB 97,998
1 2 3 4 5
ZFIN Marker ID SO ID UniProtKB ID PubMed ID ZFIN Annotation (GO/Phenotype/Expression)
ZFIN Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs
Show 6 MB 97,998
1 2 3 4 5
ZFIN Marker ID SO ID UniProtKB ID PubMed ID ZFIN Annotation (GO/Phenotype/Expression)
Sequence Coordinates Assembly: Ensembl
Show 9 MB 61,964
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Assembly: Ensembl
Show 9 MB 61,964
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Complete Assembly Clones: Ensembl
Show 359 KB 4,701
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Transgenic Insertion: ENSEMBL
Show 2 MB 15,223
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Expression: Ensembl
Show 1 MB 10,928
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Phenotype: Ensembl
Show 339 KB 3,134
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes: Ensembl
Show 4 MB 24,996
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Knockdown Reagents: Ensembl
Show 1 MB 12,094
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Sequence Data ZFIN Marker associations to Ensembl IDs
(Only associations with 1:1 relationships between ZFIN marker IDs and Ensembl IDs are stored in ZFIN. All associations can be obtained using BioMart http://www.ensembl.org/biomart/martview)
Show 1 MB 25,048
1 2 3 4
ZFIN ID Gene SO ID Symbol Ensembl ID

Externally Hosted Files:

The 'File Name'-links point to the latest version. To obtain previous versions you have to check the archive of the external source.
Category Description External Source File Name Update Frequency Format / Header
Gene Ontology Data Gene Ontology (GO) Annotations of Zebrafish Markers
(see also GO Annotation File format at the Gene Ontology Consortium) 		geneontology.org gene_association.zfin.gz weekly
Show
Anatomical Ontologies Zebrafish Anatomical Ontology in OBO Format Obofoundry zebrafish_anatomy.obo monthly OBO file format