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legumeinfo / legumemine

An InterMine which contains multiple legumes
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Add other genomic-info species from LIS that aren't currently in mines #3

Closed sammyjava closed 6 years ago

sammyjava commented 6 years ago

Cajanus cajan_ICPL87119 Vigna angularis_Gyeongwon Vigna radiata_VC1973A Trifolium pratense_MilvusB Medicago trancatula_A17 Lupinus angustifolius_Tanjil Lotus japonicus_MG20

adf-ncgr commented 6 years ago

Medicago trancatula_Mt4.0 (or is already there?)

not sure what the parenthetical question is asking, but FWIW this should be Medicago truncatula_A17 to be consistent with the use of "germplasm accession" rather than "version" naming

adf-ncgr commented 6 years ago

Also, just noticed that you are missing pigeonpea from your list above: Cajanus cajan_ICPL87119

we MAY want to create a separate PigeonpeaMine in honor of my embassy to ICRISAT in Dec.

sammyjava commented 6 years ago

Duly updated. I need to back-edit the Mt imports on other mines, no idea why I used Mt4.0 rather than the variety.

adf-ncgr commented 6 years ago

@agnespychan @vivekkrish @joannmudge @cdtown with respect to medicago naming, we will at some point need to think about how to deal with cases where the accession has both a "regular name" like A17 or R108 as well as a HapMap designation like HM341 or HM340. In some of the experiments I've done I've just made a composite name like A17_HM341 but that may be more confusing to people than helpful. I would guess that many of the hapmap accessions have nothing but an HM number, though I don't know this for sure (I just know I've never heard anyone use "regular names" for more than a handful)

joannmudge commented 6 years ago

They all have an HM number and a population. Many of them also have a line number.

http://www.medicagohapmap.org/hapmap/germplasm http://www.medicagohapmap.org/hapmap/germplasm

Joann Mudge Senior Research Scientist National Center for Genome Resources (NCGR) Santa Fe, NM 505-995-4421 jm@ncgr.org Google Scholar Page http://scholar.google.com/citations?user=Lq1fuVUAAAAJ&hl=en

On Oct 10, 2017, at 1:09 PM, adf-ncgr notifications@github.com wrote:

@agnespychan https://github.com/agnespychan @vivekkrish https://github.com/vivekkrish @joannmudge https://github.com/joannmudge @cdtown https://github.com/cdtown with respect to medicago naming, we will at some point need to think about how to deal with cases where the accession has both a "regular name" like A17 or R108 as well as a HapMap designation like HM341 or HM340. In some of the experiments I've done I've just made a composite name like A17_HM341 but that may be more confusing to people than helpful. I would guess that many of the hapmap accessions have nothing but an HM number, though I don't know this for sure (I just know I've never heard anyone use "regular names" for more than a handful)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/LegumeFederation/intermine-legumemine/issues/3#issuecomment-335576633, or mute the thread https://github.com/notifications/unsubscribe-auth/AMXtU17Tc7-pitlF1rrdVlCF06T2aIMVks5sq8D5gaJpZM4P0Wf4.

adf-ncgr commented 6 years ago

@ctcncgr someday that germplasm table will be interactive and tell us all about the data available for each of those lines...