1. The Animal QTLdb came a long way
Part I
The Animal QTLdb came a long way
(a review of criteria for the database design)
Zhiliang Hu and James Reecy
Iowa State University

3. What parameters should be set to describe a QTL?
Sensibly
Reliably
Distinctly

4. Animal info Marker / map info Traits info QTL Summary
Animals Sex Breeds Numbers Family structure Traits
Animal info
Marker/Gene Name Abbreviation Function Type Map Location Reference
Marker / map info
Trait Name Methods of measurement Data Adjustment
Traits info
Genome scan scale Model Statistical Methods Significance Test Results Figure Index
QTL Summary
A QTL Database Design schema Zhiliang Hu, ISU Sunday, May 23, 1999

5. Parameters considered
Animals: Animals Population size
Breeds Sex
Family structure etc.
Traits: Trait Name Methods of measurement
Data Adjustment etc.
Tests: Genome scan scale Model fit
Statistical methods Significance test
Statistical parameters etc.
Maps: Marker/Gene Name Type
Function Testing methods
Map Location Reference

6. Minimum parameters necessary
Trait description ( definition, measurement, classified(?) )
At least one map location ( cM location, span, anchore markers, etc. )
At least one statistics parameter ( p-value, F-value, LODs, etc. )
Animal description ( breed, origin, family, etc )
Experiment description ( breeding, tests, etc )

7. Minimum information required to sensibly describe a QTL, for records, and for meaningful comparisons -- An Animal QTLdb standard
Traits and their measurements
Trait name
Trait description
Measuring methods
Measurements
Measuring units
Test statistics
At least one of following
LOD score
P-values
F-values
Variance
Location in the genome
Species
Chromosome
Linkage map location (cm)
Linkage map Span (cm)
Experiment design *
Population
Breeding design (family structure)
Analysis methods
QTL effects *
Dominance effect
Additive effect
Candidate genes
Associated markers *
Peak marker
Flanking markers

8. Current table structures
Experiments
Exp_ID
PUBMED_ID
Animals
design
Ana_method
Software
Notes
Linkage maps
chromosome
ref_map
ref_map_uid
marker_name
location_cm
QTL
QTL_ID LocusLink_ID
QTL_symbol Chromosome
REF_MAP Position_cm
p_CI_cm FlankMark_A2
Model FlankMark_A1
LS_mean Peak_Mark
Exp_ID FlankMark_B1
LOD_score FlankMark_B2
P_values F_Statistics
VARIANCE Add_effect
trait_ID Dom_effect
PUBMED_ID Cand_gene
Traits
species
class_ID
class_name
type_ID
trait_type
trait_ID
trait_name
abbreviat
custom_name
trait_desc
measurement
scale_unit
References
ref_ID
authors
affiliatn
year
issues
title
journal
abstract

9. Frustrations
Published journal papers do NOT always have the needed information to “fit in” the database curation form
Curators often have hard time to abstract QTL evidences from some papers that have mixed QTL and “association” results for curation
Does it make sense to discriminate Mendelian genes / association results from QTL results in the QTLdb?

10. Future? A standadized “template” for publishing QTL data?
Minimum required information to reliably describe a QTL?
Recommend a criteria for publishing QTL data?
All these are for making better use of all the published QTL results, for meta-analysis, for comparative analysis, and more

11. Acknowledgement Max Rothschild (Iowa State University)
Alan Archibald, Andy Law (Roslin)
John Bastiaansen, Lizhen Wang (PIC)
Svetlana Dracheva, Wonhee Jang, Donna Maglott (NCBI)
Jack Dekkers (Iowa State University)
Gary Rohrer (USDA-MARC)
David Adelson (Texas A&M University)
Per Johnson (Sweden Göteborg University)