legumeinfo / datastore-specifications

Specifications for directory naming, file naming, file contents in the LIS datastore

legumeinfo/datastore-specifications Issues

Where do you get the validation program
Updated 5 months ago4
Gene_function readme needs a link to get_citations.pl
Closed 6 months ago6
Datastore-specification/protocols/gene_function
Closed 6 months ago1
Add gene identifier column to pan-gene set .hsh file?
Updated 7 months ago14
Specify how gene Name attributes are given
Updated 9 months ago16
RFO: associated gene collections (e.g. expression) may contain ONLY genes present in gene_models_main
Updated 9 months ago
RFO: annotation GFFs must contain Note: attribute with GO terms to be loaded into mines
Closed 9 months ago1
RFO: "gene_functions" collection
Updated a year ago13
Current pangene spec requires scientific_name_abbrev not be required; I'd like to have it.
Updated a year ago21
RFO: pangene specification and collections
Closed a year ago23
Expression data may map reads from Strain B to the genome annotation of Strain A
Closed a year ago16
RFO: add chromosome_prefix / supercontig_prefix to genome READMEs
Closed a year ago20
RFO: rename linkage groups to short names used in publications (uniqueness by genetic map reference)
Closed a year ago3
RFO: BUSCO data
Closed a year ago7
What's up with the .id_map files?
Updated 2 years ago3
mismatch between synteny spec and actual practice?
Closed 2 years ago2
RFO: add genetic_map column to qtl.tsv and qtlmrk.tsv files in QTL collections
Closed 2 years ago2
RFC: Add counts matrix to expression sets
Updated 2 years ago
RFC: split /genetic into /gwas and /qtl collections
Closed 2 years ago8
Need QC specification for each collection for file-based QC
Closed 2 years ago2
Proposal: simplified samples file for expression collections
Closed 2 years ago4
Specify data usage restrictions implementation
Updated 2 years ago2
Should we have marker FASTA collections?
Updated 2 years ago4
Create a genetic_map attribute to associate genetic collections with a single genetic map under /maps/?
Closed 2 years ago7
Specify collections under /GENUS/
Updated 2 years ago
Specify /methylation/ collections
Updated 2 years ago
Specify /traits/ collections
Updated 2 years ago
Specify /transcriptomes/ collections
Updated 2 years ago1
Specify /repeats/ collections
Updated 2 years ago1
Specify /supplements/ collections
Updated 2 years ago
Enforce mRNA-only mrna.fna files (with transcript.fna optional)
Closed 2 years ago20
Enforce ID=LIS-identifier; Name=whatever in GFFs
Closed 2 years ago5
Move /maps/ directories to /genetic/
Closed 2 years ago3
Move /qtl/ directories to /genetic/
Closed 2 years ago1
Move /gwas/ directories to /genetic/
Closed 2 years ago1
Propose "weight" field in description_genus_species to allow control of display order
Closed 3 years ago2
Specify /pangenes/ collections
Closed 3 years ago1
Specification of resources available per genome
Closed 3 years ago2
Request for clarification
Closed 3 years ago17
where are the names of the folders under species level dictated?
Closed 3 years ago8