From d7edf40d88a93a7ed1cb652a6c9541ccfc8b9b88 Mon Sep 17 00:00:00 2001
From: Adam Wright <adam.wright@wormbase.org>
Date: Tue, 15 Jun 2021 19:08:46 +0000
Subject: [PATCH] updating assemblies.json for WS280

---
 resources/ASSEMBLIES.json | 105 ++++++++++++++++++++++----------------
 1 file changed, 61 insertions(+), 44 deletions(-)

diff --git a/resources/ASSEMBLIES.json b/resources/ASSEMBLIES.json
index 2b8abb07..1cecfac5 100644
--- a/resources/ASSEMBLIES.json
+++ b/resources/ASSEMBLIES.json
@@ -1,6 +1,21 @@
 {
    "b_malayi" : {
-      "assemblies" : [],
+      "assemblies" : [
+         {
+            "appeared_in" : "WS252",
+            "assembly_accession" : "GCA_000002995.5",
+            "assembly_name" : "B_malayi-4.0",
+            "bioproject" : "PRJNA10729",
+            "bioproject_description" : "University of Pittsburgh B. malayi genome project",
+            "is_canonical" : true,
+            "laboratory" : [
+               "University of Pittsburgh, Pittsburgh, PA"
+            ],
+            "short_label" : "B_malayi-4.0",
+            "strain" : "WBStrain00041073",
+            "ucsc_name" : null
+         }
+      ],
       "full_name" : "Brugia malayi"
    },
    "c_angaria" : {
@@ -22,14 +37,6 @@
       ],
       "full_name" : "Caenorhabditis angaria"
    },
-   "c_becei" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis becei"
-   },
-   "c_bovis" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis bovis"
-   },
    "c_brenneri" : {
       "assemblies" : [
          {
@@ -124,7 +131,7 @@
             "assembly_accession" : "GCA_003052745.1",
             "assembly_name" : "Sp34_v7",
             "bioproject" : "PRJDB5687",
-            "bioproject_description" : "University of Miyazaki C. inopinata genome project",
+            "bioproject_description" : "University of Miyazaki",
             "is_canonical" : true,
             "laboratory" : [
                "Forestry and Forest Products Research Institute, Ibaraki, Japan"
@@ -162,7 +169,7 @@
             "assembly_accession" : "GCA_002259235.1",
             "assembly_name" : "CaeLat1.0",
             "bioproject" : "PRJNA248912",
-            "bioproject_description" : "University of Oregon C. latens genome project",
+            "bioproject_description" : "University of Oregon",
             "is_canonical" : true,
             "laboratory" : [
                "University of Texas, Arlington TX"
@@ -193,18 +200,6 @@
       ],
       "full_name" : "Caenorhabditis nigoni"
    },
-   "c_panamensis" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis panamensis"
-   },
-   "c_parvicauda" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis parvicauda"
-   },
-   "c_quiockensis" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis quiockensis"
-   },
    "c_remanei" : {
       "assemblies" : [
          {
@@ -220,6 +215,48 @@
             "short_label" : "WBStrain00041998",
             "strain" : "WBStrain00041998",
             "ucsc_name" : "caeRem3"
+         },
+         {
+            "appeared_in" : "WS250",
+            "assembly_accession" : "GCA_001643735.1",
+            "assembly_name" : "ASM164373v1",
+            "bioproject" : "PRJNA248909",
+            "bioproject_description" : "University of Oregon University C. remanei PX356 genome project",
+            "is_canonical" : false,
+            "laboratory" : [
+               "University of Texas, Arlington TX"
+            ],
+            "short_label" : "WBStrain00042020",
+            "strain" : "WBStrain00042020",
+            "ucsc_name" : null
+         },
+         {
+            "appeared_in" : "WS268",
+            "assembly_accession" : "GCA_001643735.2",
+            "assembly_name" : "ASM164373v2",
+            "bioproject" : "PRJNA248909",
+            "bioproject_description" : "University of Oregon University C. remanei PX356 genome project",
+            "is_canonical" : false,
+            "laboratory" : [
+               "University of Texas, Arlington TX"
+            ],
+            "short_label" : "WBStrain00042020",
+            "strain" : "WBStrain00042020",
+            "ucsc_name" : null
+         },
+         {
+            "appeared_in" : "WS268",
+            "assembly_accession" : "GCA_002259225.1",
+            "assembly_name" : "CaeRem1.0",
+            "bioproject" : "PRJNA248911",
+            "bioproject_description" : "University of Oregon University C. remanei PX439 genome project",
+            "is_canonical" : false,
+            "laboratory" : [
+               "University of Texas, Arlington TX"
+            ],
+            "short_label" : "WBStrain00042021",
+            "strain" : "WBStrain00042021",
+            "ucsc_name" : null
          }
       ],
       "full_name" : "Caenorhabditis remanei"
@@ -243,14 +280,6 @@
       ],
       "full_name" : "Caenorhabditis sinica"
    },
-   "c_sulstoni" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis sulstoni"
-   },
-   "c_tribulationis" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis tribulationis"
-   },
    "c_tropicalis" : {
       "assemblies" : [
          {
@@ -270,18 +299,6 @@
       ],
       "full_name" : "Caenorhabditis tropicalis"
    },
-   "c_uteleia" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis uteleia"
-   },
-   "c_waitukubuli" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis waitukubuli"
-   },
-   "c_zanzibari" : {
-      "assemblies" : [],
-      "full_name" : "Caenorhabditis zanzibari"
-   },
    "o_tipulae" : {
       "assemblies" : [
          {
@@ -289,7 +306,7 @@
             "assembly_accession" : "GCA_900184235.1",
             "assembly_name" : "Oscheius_tipulae_assembly_v2",
             "bioproject" : "PRJEB15512",
-            "bioproject_description" : "University of Edinburgh O. tipulae genome project",
+            "bioproject_description" : "The genome of Oscheius tipulae",
             "is_canonical" : true,
             "laboratory" : [
                "Wellcome Sanger Institute; Hinxton, United Kingdom"