Minimum information required for Animal QTLdb data entry

To ensure good data integrity and maintain high data quality standards, we request that users follow these minimum information requirements when prepare data for curation, or for batch submission, to the Animal QTLdb.

  1. Publication information - Curation Requirements: Mandatory
    • PubMed ID - For pre-publication manuscript, obtain an automatically assigned "ISU" number, which will be replaced once a PubMed ID becomes available.
    • Authors - Last names and initials for all authors
    • Author email - At least one (1) contact email; work emails are preferred
    • Affiliation - Name and location of institution(s)
    • Article title
    • Journal - Full name (with publisher information when the same name is found for another journal)
    • Year of publication
    • Issue/volume and page number - In the format the journal provides, e.g.: 8(1):123-135
    • Abstract
    • Full Text - Preferably in PDF
    • DOI - Digital Object Identifier (may be delayed but required when become available).

  2. Experiment information - Curation Requirements: Mandatory

  3. Trait information - Curation Requirements: Mandatory for QTL/association data
    • QTLdb Trait ID - QTLdb "trait_ID" that match the traits in your experiment (we may help you to find the ID if not obvious to you)
    • Trait name - The trait name used in the experiment
    • Trait abbreviation - Commonly used short forms (not arbitrary)
    • Trait description - How the trait is observed (measured)
    • Trait measurement method
    • Trait measurement unit

  4. Map information - Curation Requirements: Mandatory
    • Name and version of the map - Must be placed on, or interpolated to, one of the following:
      • Catfish:
        • (Support to genome maps pending for SNP mappings)
        • Auburn Map (Li et al. DNA Res. 2015 Feb;22(1):39-52.)
      • Cattle:
        • Btau_4.6, UMD_3.1, ARS-UCD1.2
        • USDA-MARC linkage map (Kappes et al., Genome Res. 1997. 7:235-249)
      • Chicken:
        • GG_4.0, GG_5.0
        • Wageningen linkage map (Groenen et al., Genome Res. 2000. 10:137-147)
      • Horse:
        • EC_4.0
        • Swinburne map (Genomics. 2006, 87(1):1-29) or Penedo map (Cytogenet Genome Res. 2005:111:5-15)
      • Pig:
        • SS_10.2, SS_11.1
        • USDA-MARC linkage map (Rohrer et al., Genome Res. 1996. 6:371-391)
      • Sheep:
        • OAR_3.1, OAR_4.0
        • IMF linkage map (v_4.7; Maddox et al., Genome Res. 2001, 11(7):1275-1289)
      • Rainbow Trout:
        • USDA-NCCCWA linkage map (Palti et al., Marine Biotechnology, 2012, 14(3):343-57)
    • Chromosome
    • Map locations - Curation Requirements: At least one of the following:
      • Peak/flanking Markers - peak, left, and right flanking markers (microsatellites or SNPs), see "Marker" description below
      • Linkage map Coordinates - in 'cM', peak and span
      • Genome map Coordinates - in 'bp', usually a span, occasionally a point location
      • Linkage marker - Must be on a linkage map
      • SNP:
        • SNP in dbSNP, mapped: MUST have a dbSNP 'rs' number
        • SNP not in dbSNP, mapped: Need a map location on a known assembly ; if mapped to a private assembly, must have flanking sequences or probe sequences
        • SNP not in dbSNP, un-mapped: must have flanking sequences or probe sequences

  5. Statistical support - Curation Requirements: At least one of the following:
    • Bayes value
    • F Statistics
    • Likelihood ratio
    • LOD score
    • LS mean
    • P values: e.g. "0.003274" OR "3.274000e-03". Any -log10 "p-values" must be converted back to its original form before they can be entered into the QTLdb.
    • VARIANCE
    • Posterior Probablity of Inclusion
    • iHS - Signature of Selection test: Log ratio between two integrated haplotype homozygosity scores
    • CLR - Signature of Selection test: Multilocus composite likelihood ratio test.
    • XPCLR - Signature of Selection test: Cross-population composite likelihood ratio test (multilocus allele frequency differentiation between two populations).
    • EHH - Signature of Selection test: Extended haplotype homozygosity
    • XPEHH - Signature of Selection test: Cross-population extended haplotype homozygosity

  6. Core Information - Curation Requirements: At least one of the following:
    • QTL/Association Data
      • Map Location
      • Trait Linked
      • Statistical evidence - Data accepted only when it reaches a suggestive or significant level
      • Phenotypic/SNP effect - May be allele specific; optional. e.g. Dominance effect, Additive effect
    • eQTL Data - expression QTL
      • Map location
      • Trait or Gene Linked
      • Statistical evidence - Only significant data are accepted

    • CNV Data - copy number variation
      • Map Location
      • Type - Gain/Loss
      • Validation - Yes/No
      • Breed - Associated
      • Statistical Evidence - Only significant data is accepted

    • Signature of Selection Data
      • Map Location
      • Breed or Line - Specify which allele is associated
      • Statistical Evidence - Only significant data are accepted

    • Epistasis Data
      • Pre-request: - Must be between two or more existing QTL
      • Statistical evidence - only significant data are accepted

    • Pleiotropy data
      • Pre-request: - Must be between two or more existing QTL
      • Statistical Evidence - Only significant data are accepted

    • Haplotype data
      • Pre-request: - Must be between two or more existing QTL/SNPs
      • Statistical Evidence - Only significant data are accepted

  7. Additional information - Curation Requirements: Where applicable
    • Gene ID - Must be one of the following:
      • NCBI GeneDB Gene_ID
      • Ensembl Gene_ID
      • HGNC Gene_ID
    • Gene networks
Download the Excel templates
First draft: October 12, 2015 11:41:58
Updated: August 19, 2017 21:38:46
Last updated: August 31, 2021 11:04:39

 

© 2003-2024: USA · USDA · NRPSP8 · Program to Accelerate Animal Genomics Applications. Contact: Bioinformatics Team