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datastore-specifications
Specifications for directory naming, file naming, file contents in the LIS datastore
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RFO: Restructure, formalize, and validate MANIFEST files
#50
StevenCannon-USDA
opened
1 month ago
5
Update qtl.md
#49
jd-campbell
closed
1 month ago
0
Where do you get the validation program
#48
maxglycine
closed
1 month ago
5
Datastore-specification/protocols/gene_function
#47
maxglycine
closed
5 months ago
1
Gene_function readme needs a link to get_citations.pl
#46
maxglycine
closed
5 months ago
6
Add gene identifier column to pan-gene set .hsh file?
#45
sammyjava
opened
7 months ago
14
Specify how gene Name attributes are given
#44
sammyjava
opened
9 months ago
16
RFO: associated gene collections (e.g. expression) may contain ONLY genes present in gene_models_main
#43
sammyjava
opened
9 months ago
0
RFO: annotation GFFs must contain Note: attribute with GO terms to be loaded into mines
#42
sammyjava
closed
9 months ago
1
Current pangene spec requires scientific_name_abbrev not be required; I'd like to have it.
#41
sammyjava
closed
1 month ago
22
RFO: "gene_functions" collection
#40
StevenCannon-USDA
opened
1 year ago
13
RFO: pangene specification and collections
#39
StevenCannon-USDA
closed
1 year ago
23
RFO: add chromosome_prefix / supercontig_prefix to genome READMEs
#38
sammyjava
closed
1 year ago
20
RFO: BUSCO data
#37
adf-ncgr
closed
1 year ago
7
mismatch between synteny spec and actual practice?
#34
adf-ncgr
closed
1 year ago
2
RFO: add genetic_map column to qtl.tsv and qtlmrk.tsv files in QTL collections
#33
sammyjava
closed
1 year ago
2
RFC: Add counts matrix to expression sets
#32
sammyjava
opened
1 year ago
0
What's up with the .id_map files?
#31
sammyjava
closed
1 month ago
3
RFO: rename linkage groups to short names used in publications (uniqueness by genetic map reference)
#30
sammyjava
closed
1 year ago
3
RFC: split /genetic into /gwas and /qtl collections
#29
sammyjava
closed
1 year ago
8
27 proposal simplified samples file for expression collections
#28
sammyjava
closed
1 year ago
0
Proposal: simplified samples file for expression collections
#27
sammyjava
closed
1 year ago
4
Expression data may map reads from Strain B to the genome annotation of Strain A
#26
sammyjava
closed
1 year ago
16
Specify data usage restrictions implementation
#25
sammyjava
opened
2 years ago
2
Should we have marker FASTA collections?
#24
sammyjava
opened
2 years ago
4
Create a genetic_map attribute to associate genetic collections with a single genetic map under /maps/?
#23
sammyjava
closed
2 years ago
7
Enforce ID=LIS-identifier; Name=whatever in GFFs
#22
sammyjava
closed
2 years ago
5
Enforce mRNA-only mrna.fna files (with transcript.fna optional)
#21
sammyjava
closed
2 years ago
20
Propose "weight" field in description_genus_species to allow control of display order
#20
StevenCannon-USDA
closed
2 years ago
2
Specify /supplements/ collections
#19
sammyjava
opened
2 years ago
0
Specify /traits/ collections
#18
sammyjava
opened
2 years ago
0
Specify /methylation/ collections
#17
sammyjava
opened
2 years ago
0
Specify collections under /GENUS/
#16
sammyjava
opened
2 years ago
0
formally disallowing underscores in genus and species; require first …
#15
adf-ncgr
closed
2 years ago
1
extended character class for gensp regex
#14
adf-ncgr
closed
2 years ago
0
Added null to optional fields; quoted dates so they validate; added sraproject.
#13
sammyjava
closed
2 years ago
3
a fairly simplistic json-schema file for our README.yml files
#12
adf-ncgr
closed
2 years ago
3
Specify /pangenes/ collections
#11
sammyjava
closed
2 years ago
1
Move /qtl/ directories to /genetic/
#10
sammyjava
closed
2 years ago
1
Move /gwas/ directories to /genetic/
#9
sammyjava
closed
2 years ago
1
Move /maps/ directories to /genetic/
#8
sammyjava
closed
2 years ago
3
Specification of resources available per genome
#6
sammyjava
closed
2 years ago
2
Need QC specification for each collection for file-based QC
#5
sammyjava
closed
1 year ago
2
Specify /transcriptomes/ collections
#4
sammyjava
opened
3 years ago
1
Specify /repeats/ collections
#3
adf-ncgr
opened
3 years ago
1
where are the names of the folders under species level dictated?
#2
adf-ncgr
closed
3 years ago
8
Request for clarification
#1
adf-ncgr
closed
2 years ago
17