From a3159b54620b045279836ffb75a512cfe5a5db48 Mon Sep 17 00:00:00 2001
From: Chris Mungall <cjm@berkeleybop.org>
Date: Fri, 22 Jan 2016 10:52:54 -0800
Subject: [PATCH] adding config to auto-insert ontology header tags for legacy
 ontologies. See #204 for details

---
 ontology/bila.md    | 1 +
 ontology/bto.md     | 1 +
 ontology/ddpheno.md | 1 +
 ontology/emap.md    | 1 +
 ontology/fao.md     | 1 +
 ontology/fbsp.md    | 2 +-
 ontology/fma.md     | 1 +
 ontology/mfo.md     | 1 +
 ontology/mod.md     | 1 +
 ontology/mpath.md   | 1 +
 ontology/rex.md     | 1 +
 ontology/spd.md     | 1 +
 12 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/ontology/bila.md b/ontology/bila.md
index f7cfc473a..9acf9350f 100644
--- a/ontology/bila.md
+++ b/ontology/bila.md
@@ -15,6 +15,7 @@ title: Bilateria anatomy
 build:
   source_url: http://4dx.embl.de/4DXpress_4d/edocs/bilateria_mrca.obo
   method: obo2owl
+  insert_ontology_id: true
 is_obsolete: true
 replaced_by: uberon
 ---
diff --git a/ontology/bto.md b/ontology/bto.md
index 2fd3acb99..bd2ca9ee4 100644
--- a/ontology/bto.md
+++ b/ontology/bto.md
@@ -20,6 +20,7 @@ license:
 title: BRENDA tissue / enzyme source
 build:
   source_url: http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO
+  insert_ontology_id: true
   method: obo2owl
 ---
 
diff --git a/ontology/ddpheno.md b/ontology/ddpheno.md
index 6dbb0e173..1cc652993 100644
--- a/ontology/ddpheno.md
+++ b/ontology/ddpheno.md
@@ -16,6 +16,7 @@ taxon:
 title: Dictyostelium discoideum phenotype
 build:
   source_url: https://raw.githubusercontent.com/dictyBase/migration-data/master/ontologies/dicty_phenotypes.obo
+  insert_ontology_id: true
   method: obo2owl
 ---
 
diff --git a/ontology/emap.md b/ontology/emap.md
index f7b19df0d..0bfb8d072 100644
--- a/ontology/emap.md
+++ b/ontology/emap.md
@@ -17,6 +17,7 @@ title: Mouse gross anatomy and development, timed
 build:
   notes: new url soon
   source_url: ftp://ftp.hgu.mrc.ac.uk/pub/MouseAtlas/Anatomy/EMAP_combined.obo
+  insert_ontology_id: true
   method: obo2owl
 used_by:
  - url: https://www.biosharing.org/biodbcore-000659
diff --git a/ontology/fao.md b/ontology/fao.md
index 9b4a530c9..20e67998c 100644
--- a/ontology/fao.md
+++ b/ontology/fao.md
@@ -16,6 +16,7 @@ taxon:
 title: Fungal gross anatomy
 build:
   source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/fungi/fungal_anatomy.obo
+  insert_ontology_id: true
   method: obo2owl
 ---
 
diff --git a/ontology/fbsp.md b/ontology/fbsp.md
index e96ee6a97..41ddea368 100644
--- a/ontology/fbsp.md
+++ b/ontology/fbsp.md
@@ -16,7 +16,7 @@ title: Fly taxonomy
 build:
   source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/taxonomy/fly_taxonomy.obo
   method: obo2owl
-
+  insert_ontology_id: true
 is_obsolete: true
 ---
 
diff --git a/ontology/fma.md b/ontology/fma.md
index 04f2d91c2..9899f0328 100644
--- a/ontology/fma.md
+++ b/ontology/fma.md
@@ -20,6 +20,7 @@ taxon:
 title: Foundational Model of Anatomy (subset)
 build:
   source_url: http://svn.code.sf.net/p/obo/svn/fma-conversion/trunk/fma2_obo.obo
+  insert_ontology_id: true
   method: obo2owl
 tracker: https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/
 ---
diff --git a/ontology/mfo.md b/ontology/mfo.md
index 68c2beeee..7075e47ec 100644
--- a/ontology/mfo.md
+++ b/ontology/mfo.md
@@ -15,6 +15,7 @@ title: Medaka fish anatomy and development
 build:
   source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/medaka_ontology.obo
   method: obo2owl
+  insert_ontology_id: true
 ---
 
 A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, <i>Oryzias latipes</i>.
diff --git a/ontology/mod.md b/ontology/mod.md
index 3181f34e2..a224464dc 100644
--- a/ontology/mod.md
+++ b/ontology/mod.md
@@ -12,6 +12,7 @@ products:
 title: Protein modification
 build:
   source_url: https://raw.githubusercontent.com/MICommunity/psidev/master/psi/mod/data/PSI-MOD.obo
+  insert_ontology_id: true
   method: obo2owl
 ---
 
diff --git a/ontology/mpath.md b/ontology/mpath.md
index 80fd9f6db..1ceeb4d8d 100644
--- a/ontology/mpath.md
+++ b/ontology/mpath.md
@@ -19,6 +19,7 @@ license:
   label: CC-BY
 build:
   source_url: https://raw.githubusercontent.com/PaulNSchofield/mpath/master/mpath.obo
+  insert_ontology_id: true
   method: obo2owl
 ---
 
diff --git a/ontology/rex.md b/ontology/rex.md
index cd439775a..4fbfec730 100644
--- a/ontology/rex.md
+++ b/ontology/rex.md
@@ -10,6 +10,7 @@ products:
 title: Physico-chemical process
 build:
   source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/physicochemical/rex.obo
+  insert_ontology_id: true
   method: obo2owl
 ---
 
diff --git a/ontology/spd.md b/ontology/spd.md
index af5a77e0e..fdfddc1cc 100644
--- a/ontology/spd.md
+++ b/ontology/spd.md
@@ -16,6 +16,7 @@ title: Spider Ontology
 build:
   source_url: http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/spider/spider_comparative_biology.obo
   method: obo2owl
+  insert_ontology_id: true
 tracker: http://sourceforge.net/tracker/?group_id=76834&atid=977401
 ---