Table 1.

Data Types in ZFIN

Data Category	Data Types	Metadata
Sequence Features	genes, pseudogenes, microRNAs, transcripts, BACs, PACs, fosmids, cDNA clones, ESTs, morpholinos, SSLPs, RAPDs, STSs, engineered regions and foreign genes	chromosomal location, mapping data, relationships between sequence features, sequence accession IDs
Alleles and Variations	insertions, point mutations, inversions, transgenic insertions, translocations, deletions, small deletions, substitutions, indels, SNPs, allele designations	genotype zygosity, chromosomal location, availability from resource centers and labs, mapping data
Sequence Targeting Reagents	morpholinos, CRISPRs and TALENs	sequences, phenotypes and expression in fish treated with reagent, genotypes created with reagent, transgenic constructs used to create transgenic insertions
Transgenic Constructs and Lines	Transgenic constructs, line designations	relationships between sequence features, genotype zygosity, availability from resource centers and labs, expression and phenotype data, transgenic constructs used to create transgenic insertions
Phenotypes	phenotype curated from papers and loaded through collaborations with users providing phenotype data	developmental stage, experimental conditions, genotype, anatomy, GO, MPATH, spatial and quality ontology terms
Genotypes	single/double/triple/etc. mutants, transgenic fish, wild-types, complex rearrangements, morpholino/TALEN/CRISPR genotypes	parental genotype, phenotypes and expression that use genotypes, genotype availability from resource centers and labs
Gene Expression	expression curated from papers and loaded through collaborations with users providing expression data	genotype, experimental conditions, developmental stage, anatomical structures, image sizes, dimensions, and contents, captions and labels for phenotypes and expression that use figures/images
Antibodies	gene expression patterns and antibody staining patterns	labeled cellular and anatomical structures, stages, targeted genes, sources and availability, host organism, antibody type and isotype, assays
Experimental Conditions	changes to temperature, salinity, chemical, etc. conditions	Specifics about experimental conditions such as increased or decreased temperature, which chemical was used, etc., phenotypes, expression that use the experimental condition
Ontologies	gene ontology (GO), quality, anatomy, MPATH neoplasms, spatial, developmental stage ontology, UBERON (Mine only), MEDIC (Mine only)	terms for phenotype, expression, and gene data, term definition, relationships between terms
Homologues	curated zebrafish homologues in mouse, human, and fly, predicted homologues from the PANTHER data source (Mine only)	homologue names, symbols and chromosome locations, human disease information from OMIM
Data Sources	publications, laboratories, companies, people	names, PubMed IDs, addresses, phone numbers, reagents, allele registrations, web sites, lab members
Nomenclature	genes, pseudogenes, transgenics, mutants, constructs	line designations, gene names
Figures, Images, Movies	expression and phenotype images from publications, user submitted images and movies, images of people, labs and companies	image sizes, dimensions, and contents, captions and labels for phenotypes and expression that use figures/images
Links to Other Databases	NCBI (Gene, RefSeq, GenPept, UniGene, UniSTS, dbSNP, PubMed), OMIM, Wellcome Trust Sanger Institute (Vega, Ensembl, ZMP), MGI, FlyBase, UniProtKB, InterPro, Pfam, PROSITE, GEO, EBI, NCBO-CARO, UCSC, CreZoo, miRBASE, Addgene, MODB, Zfishbook	length and types of sequences in other databases, plasmids, protein domains

Acronyms and abbreviations used in Table 1: Addgene: non-profit plasmid repository www.addgene.org; BAC: Bacterial Artificial Chromosome; cDNA: Complementary DNA; CreZoo: database of zebrafish CreER driver lines https://crezoo.crt-dresden.de/crezoo/; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats knockdown reagent; dbSNP: NCBI Short Genetic Variations database http://www.ncbi.nlm.nih.gov/SNP; EBI: European Bioinformatics Institute http://www.ebi.ac.uk/; Ensembl; automatically annotated eukaryotic genomes http://www.ensembl.org; EST: Expressed Sequence Tag; FlyBase: Drosophila model organism database http://flybase.org/; GenPept; NCBI Protein Sequence Database; GEO: Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/; GO: Gene Ontology; InterPro: Integrated Resource of Protein Domains and Functional Sites http://www.ebi.ac.uk/interpro/; MEDIC: disease vocabulary that includes MeSH (Medical Subject Headings) and OMIM disease terms; MGI: Mouse Genome Informatics http://www.informatics.jax.org; miRBase: miRNA sequence and annotation database http://www.mirbase.org/; MODB: MOrpholino Database http://www.morpholinodatabase.org; MPATH: Mouse Pathology Ontology; NCBI: National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/; NCBO-CARO: National Center for Biomedical Ontology - Common Anatomy Reference Ontology); OMIM: Online Mendelian Inheritance in Man http://www.ncbi.nlm.nih.gov/omim; PAC: P1 bacterophage Artificial Chromosome; PANTHER: Protein Analysis Through Evolutionary Relationships database http://pantherdb.org/; Pfam: Protein Families Database http://pfam.xfam.org/; PROSITE: Database of protein families and domains http://prosite.expasy.org/; PubMed: NCBI literature database http://www.ncbi.nlm.nih.gov/pubmed; RAPD: Rapid amplified polymorphic DNA; RefSeq: NCBI Reference Sequence database http://www.ncbi.nlm.nih.gov/refseq/; SSLP:Simple Sequence Length Polymorphism; STS: Sequence Tagged Site; TALEN: TAL Effector Nuclease; UBERON: cross-species “Uber-anatomy” ontology; UCSC: University of California Santa Cruz genome bioinformatics http://genome.ucsc.edu; UniGene: Non-redundant set of genes at NCBI http://www.ncbi.nlm.nih.gov/unigene; UniProtKB: Universal Protein Resource Knowledgebase http://www.uniprot.org/help/uniprotkb; UniSTS; NCBI STS database, contents now in Probe database; Vega: Vertebrate Genome Annotation Database http://vega.sanger.ac.uk; Zfishbook: Zebrafish protein trap consortium database http://zfishbook.org/; ZMP; Zebrafish Mutation Project at the Sanger Institute http://www.sanger.ac.uk/resources/zebrafish/zmp/