Update READMEs for pangene collections for compliance with validate.s…

…h (adding scientific_name_abbrev)
legumeinfo · Mar 22, 2024 · 3f3488e · 3f3488e
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Showing 16 changed files with 31 additions and 13 deletions.
diff --git a/Arachis/GENUS/pangenes/Arachis.pan2.5P1K/README.Arachis.pan2.5P1K.yml b/Arachis/GENUS/pangenes/Arachis.pan2.5P1K/README.Arachis.pan2.5P1K.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Arachis species, based on A. hypogaea, A. duranensis,
 
 scientific_name: Arachis
 
+scientific_name_abbrev: Arachis
+
 taxid: 3826
 
 annotations_main:

diff --git a/Arachis/GENUS/pangenes/Arachis.pan3.BYQ9/README.Arachis.pan3.BYQ9.yml b/Arachis/GENUS/pangenes/Arachis.pan3.BYQ9/README.Arachis.pan3.BYQ9.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Arachis species, based on A. hypogaea, A. duranensis,
 
 scientific_name: Arachis
 
+scientific_name_abbrev: Arachis
+
 taxid: 3826
 
 annotations_main:

diff --git a/...his/hypogaea/genome_alignments/BaileyII.gnm1.wga.Z93X/CHECKSUM.BaileyII.gnm1.wga.Z93X.md5 b/...his/hypogaea/genome_alignments/BaileyII.gnm1.wga.Z93X/CHECKSUM.BaileyII.gnm1.wga.Z93X.md5
@@ -2,6 +2,7 @@
 fc53e193da13e2d6611fc5787b38f032  ./arahy.BaileyII.gnm1.x.araca.K10017.gnm1.Z93X.paf.gz
 4df0c59ab813da15f339ac094554a94b  ./arahy.BaileyII.gnm1.x.araip.K30076.gnm2.Z93X.bam.bai
 7d6297c86ed70c77909a278c45b3ad99  ./arahy.BaileyII.gnm1.x.aradu.V14167.gnm2.Z93X.bam.bai
+4f0a1906cb29d17e1f0de5a50e056cd1  ./README.BaileyII.gnm1.wga.Z93X.yml
 88189f7433ebaf6633bb49189cdff0be  ./arahy.BaileyII.gnm1.x.araip.K30076.gnm2.Z93X.bam
 619754e79ac5a5721c64f96253cac7ec  ./arahy.BaileyII.gnm1.x.aradu.V14167.gnm2.Z93X.paf.gz
 8726ca47d2c36ef4efb6569cd75e6809  ./arahy.BaileyII.gnm1.x.aradu.V14167.gnm2.Z93X.bam

diff --git a/Arachis/ipaensis/genome_alignments/K30076.gnm2.wga.08ZF/README b/Arachis/ipaensis/genome_alignments/K30076.gnm2.wga.08ZF/README
@@ -1,11 +1,12 @@
-identifier: K30076.gnm2.wga.08ZF  
+identifier: BaileyII.gnm1.wga.Z93X
 
-provenance: The files in this dir originated from alignment of the two genomes below at PeanutBase/LIS.
-Used minimap2(script:run_minimap2_genome.bash) between araip.K30076.gnm2.1GWY.genome_main.fna.gz (Ref) and araca.K10017.gnm1.DQ4M.genome_main.fna.gz(Qry). 
+provenance: The files in this dir originated from alignment of genomes below at PeanutBase/LIS.
+Used minimap2(script:run_minimap2_genome.bash) between BaileyII.gnm1.1JTF (Ref) and other genomes as Qry.
 
-synopsis: araip.K30076.gnm2-x-araca.K10017.gnm1
+synopsis: Genome alignments with BaileyII.gnm1.1JTF
 
-description:
+description: The files in this dir originated from alignment of genomes below at PeanutBase/LIS.
+Used minimap2(script:run_minimap2_genome.bash) between BaileyII.gnm1.1JTF (Ref) and other genomes as Qry.
 
 data_curators: Sudhansu Dash
 
diff --git a/Cicer/GENUS/pangenes/Cicer.pan2.CMWZ/README.Cicer.pan2.CMWZ.yml b/Cicer/GENUS/pangenes/Cicer.pan2.CMWZ/README.Cicer.pan2.CMWZ.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Cicer species, based on C. arietinum, C. echinospermu
 
 scientific_name: Cicer
 
+scientific_name_abbrev: Cicer
+
 taxid: 3826
 
 annotations_main:

diff --git a/Cicer/GENUS/pangenes/Cicer.pan3.JVTK/README.Cicer.pan3.JVTK.yml b/Cicer/GENUS/pangenes/Cicer.pan3.JVTK/README.Cicer.pan3.JVTK.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Cicer species, based on C. arietinum, C. echinospermu
 
 scientific_name: Cicer
 
+scientific_name_abbrev: Cicer
+
 taxid: 3826
 
 annotations_main:

diff --git a/Glycine/GENUS/pangenes/Glycine.pan4.RK4P/README.Glycine.pan4.RK4P.yml b/Glycine/GENUS/pangenes/Glycine.pan4.RK4P/README.Glycine.pan4.RK4P.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Glycine species, based on G. max and G. soja but also
 
 scientific_name: Glycine
 
+scientific_name_abbrev: Glycine
+
 taxid: 3846
 
 annotations_main:

diff --git a/Glycine/GENUS/pangenes/Glycine.pan5.MKRS/README.Glycine.pan5.MKRS.yml b/Glycine/GENUS/pangenes/Glycine.pan5.MKRS/README.Glycine.pan5.MKRS.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Glycine species, based on G. max and G. soja but also
 
 scientific_name: Glycine
 
+scientific_name_abbrev: Glycine
+
 taxid: 3846
 
 annotations_main:

diff --git a/Medicago/GENUS/pangenes/Medicago.pan2.451K/README.Medicago.pan2.451K.yml b/Medicago/GENUS/pangenes/Medicago.pan2.451K/README.Medicago.pan2.451K.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Medicago species, based primarily on M. truncatula bu
 
 scientific_name: Medicago
 
+scientific_name_abbrev: Medicago
+
 taxid: 3877
 
 annotations_main:

diff --git a/Medicago/GENUS/pangenes/Medicago.pan3.9X6B/README.Medicago.pan3.9X6B.yml b/Medicago/GENUS/pangenes/Medicago.pan3.9X6B/README.Medicago.pan3.9X6B.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Medicago species, based primarily on M. truncatula bu
 
 scientific_name: Medicago
 
+scientific_name_abbrev: Medicago
+
 taxid: 3877
 
 annotations_main:

diff --git a/Medicago/truncatula/annotations/HM078.gnm1.ann1.3RNP/README.HM078.gnm1.ann1.3RNP.yml b/Medicago/truncatula/annotations/HM078.gnm1.ann1.3RNP/README.HM078.gnm1.ann1.3RNP.yml
@@ -24,12 +24,8 @@ original_file_creation_date: "2024-01-02"
 
 local_file_creation_date: "2024-01-11"
 
-publication_doi: 
-
 dataset_release_date: "2024-01-11"
 
-publication_title: 
-
 contributors: "Jacob Botkin, Shaun Curtin"
 
 data_curators: Andrew Farmer

diff --git a/Medicago/truncatula/genomes/HM078.gnm1.Q3TM/README.HM078.gnm1.Q3TM.yml b/Medicago/truncatula/genomes/HM078.gnm1.Q3TM/README.HM078.gnm1.Q3TM.yml
@@ -26,12 +26,8 @@ original_file_creation_date: "2024-01-02"
 
 local_file_creation_date: "2024-01-11"
 
-publication_doi: 
-
 dataset_release_date: "2024-01-11"
 
-publication_title: 
-
 contributors: "Jacob Botkin, Shaun Curtin"
 
 data_curators: Andrew Farmer

diff --git a/Phaseolus/GENUS/pangenes/Phaseolus.pan2.G5HV/README.Phaseolus.pan2.G5HV.yml b/Phaseolus/GENUS/pangenes/Phaseolus.pan2.G5HV/README.Phaseolus.pan2.G5HV.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Phaseolus species, based primarily on P. vulgaris but
 
 scientific_name: Phaseolus
 
+scientific_name_abbrev: Phaseolus
+
 taxid: 3883
 
 annotations_main:

diff --git a/Phaseolus/GENUS/pangenes/Phaseolus.pan3.LXKV/README.Phaseolus.pan3.LXKV.yml b/Phaseolus/GENUS/pangenes/Phaseolus.pan3.LXKV/README.Phaseolus.pan3.LXKV.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Phaseolus species, based primarily on P. vulgaris but
 
 scientific_name: Phaseolus
 
+scientific_name_abbrev: Phaseolus
+
 taxid: 3883
 
 annotations_main:

diff --git a/Vigna/GENUS/pangenes/Vigna.pan2.MQQM/README.Vigna.pan2.MQQM.yml b/Vigna/GENUS/pangenes/Vigna.pan2.MQQM/README.Vigna.pan2.MQQM.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Vigna species, based primarily on V. unguiculata but
 
 scientific_name: Vigna
 
+scientific_name_abbrev: Vigna
+
 taxid: 3913
 
 annotations_main:

diff --git a/Vigna/GENUS/pangenes/Vigna.pan3.V294/README.Vigna.pan3.V294.yml b/Vigna/GENUS/pangenes/Vigna.pan3.V294/README.Vigna.pan3.V294.yml
@@ -9,6 +9,8 @@ synopsis: "Pangene set for Vigna species, based primarily on V. unguiculata but
 
 scientific_name: Vigna
 
+scientific_name_abbrev: Vigna
+
 taxid: 3913
 
 annotations_main: