pig QTLdb data description

Data set metadata

Dataset title: pig QTLdb

Dataset description: Pig Quantitative Trait Locus (QTL) Database (Pig QTLdb), which is part of the Animal QTLdb, contains pig QTL and association data curated from published data. The database is designed to facilitate the process for users to compare, confirm, and locate the most plausible location for genes responsible for quantitative traits important to pig production.

Download URL: http://www.animalgenome.org/cgi-bin/QTLdb/SS/download?file=gbpSS_10.2

• Note: This is an indirect link as the actual GFF file name changes with the session.

Release/version: 30

Release issue date: 29-08-2016

License: ?

Distribution format: GFF3

• Note: Strictly speaking, the file does not comply with the latest spec.

MD5 checksum: 201bc6689eae8f2da843e27b370a2eac

Data record metadata

Example:

Chr.1   Animal QTLdb    Meat_and_Carcass_Association    155977038   156168386   .   .   .   QTL_ID=10628;Name=Backfat at tenth rib;Abbrev=10RIBBFT;PUBMED_ID=12807784;trait_ID=7;trait=Backfat at tenth rib;FlankMarkers;VTO_name=subcutaneous adipose thickness;CMO_name=back fat thickness, 10th rib;Map_Type=Linkage;Model=Mendelian;peak_cM=76;Significance=Significant;P-value=<0.0001;Additive_Effect=0.06;gene_ID=397359;gene_IDsrc=NCBIgene

GFF3 files are nine-column, tab-delimited, plain text files:

Column 1 "seqid": pig chromosome numbers (e.g. Chr.[0-9,X,Y)], mandatory Note: Link the chromosome numbers to RefSeq accessions (e.g. Chr.1 -> NC_010443)

Column 2 "source": data source name (Animal QTLdb), mandatory

Column 3 "type": association/QTL type, optional Note: Use of non-standard feature types in this field (e.g. Reproduction_Association) that group QTLs into categories.

Column 4 "start": start coordinate of the QTL region on a chromosome

Column 5 "end": end coordinate of the QTL region on a chromosome

Column 6 "score": not available

Column 7 "strand": not applicable

Column 8 "phase": not applicable

Column 9 "attributes": key=value pairs separated by ';', mandatory keys:

• QTL_ID

• PUBMED_ID: evidence for QTL/association in literature

• CMO_name: link to terms in Clinical Measurement Ontology (CMO, http://obofoundry.org/ontology/cmo.html)

• VTO_name: link to terms in Vertebrate Trait ontology (VT, http://obofoundry.org/ontology/vt.html)

• PTO_name: link to terms in Livestock Product Trait ontology (LPT, https://bioportal.bioontology.org/ontologies/LPT)

• breed

• FlankMarkers

• Additive_Effect

• Dominance_Effect

• Bayes-value

• Likelihood_Ratio

• LOD-score

• F-Stat

• Variance

• Map_Type

• Model

• P-value

• gene_ID: NCBI Gene ID

Note: Unfortunately, LPT/VT/CMO term IDs are not provided along the names so these need to be mapped/reconciled.