Merge branch 'master' into lschriml-patch-2

Author: deepakunni3

docs/SOP.md

@@ -12,6 +12,7 @@ This document contains standard operating procedures (SOPs) for the OBO Foundry
 - [Notification of NOR Decision](#NOD)
 - [Changing ontology metadata in the registry](#META)
 - [Reviving obsolete, orphaned, or inactive ontologies](#REACTIVATION)
+- [Adding new members to obo-discuss](#OBO_DISCUSS)
 - [Becoming a member of the OBO Operations Committee](#OPS_MEMBER)
 - [Chairing an OBO Operations Committee meeting call](#OPS_CHAIR)
 
@@ -143,6 +144,14 @@ Currently, these are the required steps:
 1. If there is no significant objection within a four week time period, the status change is enacted by merging the pull request.
 1. The contact person for the ontology should be notified of the acceptance or rejection of the change.
 
+## Adding new members to obo-discuss
+<a name="OBO_DISCUSS"></a>
+
+OBO Discuss is a Google Group: https://groups.google.com/g/obo-discuss. Anyone with an email address can ask to join OBO Discuss, but we have had trouble with spammers in the past, so the Google Group is configured to require new members to be approved by one of the mailing list owners.
+Some of the mailing list owners filter the Pending Members list every few days. Checking the Pending Members was also part of the Operations chairing instructions, to remind us to do it every two weeks, at a minimum.
+
+When someone asks to join, they must include an email address and they may provide a reason that they want to join. If they provide a reason that's not gibberish, we accept them. If they don't, we search Google for their email address. If there are good results (often from a university or company), we accept. If nothing suitable turns up, we email the applicant and explain that everyone is welcome but we filter for spammers. We usually get a reply and then click "Accept". (If they don't reply, then we don't accept them in the group.)
+
 <a name="OPS_MEMBER"></a>
 
 ## Becoming a member of the OBO Operations Committee

ontology/oostt.md

@@ -18,6 +18,19 @@ products:
 - id: oostt.owl
 repository: https://github.com/OOSTT/OOSTT
 tracker: https://github.com/OOSTT/OOSTT/issues
+usages:
+- description: OOSTT terms, such as OOSTT_00000017 'trauma program' and OOSTT_00000021 'trauma medical director role,' are used in the CAFE questionnaire to assess trauma centers and systems.
+  type: application
+  user: https://cafe-trauma.com/
+- description: OOSTT terms, such as OOSTT_00000002 'trauma center' and OOSTT_00000066 'emergency medicine liaison role,' are used in the TIPTOE questionnaire to relate trauma center/system structure to patient outcomes.
+  type: application
+  user: https://tiptoe.apps.dbmi.cloud/tiptoe
+- description: Terms from OOSTT are imported and used by OMRSE.
+  examples:
+  - description: academic degree
+    url: http://purl.obolibrary.org/obo/OOSTT_00000074
+  type: owl:Ontology
+  user: https://github.com/mcwdsi/OMRSE
 activity_status: active
 ---
 

ontology/symp.md

@@ -5,15 +5,15 @@ title: Symptom Ontology
 build:
   infallible: 1
   method: obo2owl
-  source_url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/symp.obo
+  source_url: https://raw.githubusercontent.com/DiseaseOntology/SymptomOntology/master/src/ontology/symp.obo
 contact:
   email: lynn.schriml@gmail.com
   github: lschriml
   label: Lynn Schriml
   orcid: 0000-0001-8910-9851
 description: An ontology of disease symptoms, with symptoms encompasing perceived changes in function, sensations or appearance reported by a patient indicative of a disease.
 domain: health
-homepage: http://symptomontologywiki.igs.umaryland.edu/mediawiki/index.php/Main_Page
+homepage: https://github.com/DiseaseOntology/SymptomOntology
 license:
   label: CC0 1.0
   url: https://creativecommons.org/publicdomain/zero/1.0/
@@ -37,8 +37,8 @@ usages:
 - description: Symptoms of human diseases in the DO
   examples:
   - description: symptoms of human diseases
-    url: http://www.disease-ontology.org/?id=DOID:0060164
-  user: http://www.disease-ontology.org
+    url: https://disease-ontology.org/?id=DOID:0060164
+  user: https://disease-ontology.org/
 activity_status: active
 ---
 

ontology/trans.md

@@ -31,12 +31,12 @@ tags:
 - disease
 tracker: https://github.com/DiseaseOntology/PathogenTransmissionOntology/issues
 usages:
-- description: Methods of trnasmission of human diseases in the DO
+- description: Methods of transmission of human diseases in the DO
   examples:
   - description: methods of transmission of human diseases
-    url: http://www.disease-ontology.org/?id=DOID:12365
-  user: http://www.disease-ontology.org
+    url: https://disease-ontology.org/?id=DOID:12365
+  user: https://disease-ontology.org/
 activity_status: active
 ---
 
-The Pathogen Transmission Ontology describes the tranmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.
+The Pathogen Transmission Ontology describes the transmission methods of human disease pathogens describing how a pathogen is transmitted from one host, reservoir, or source to another host. The pathogen transmission may occur either directly or indirectly and may involve animate vectors or inanimate vehicles.

resources.md

@@ -34,7 +34,7 @@ title: Ontology Tools and Resources
 - [ROBOT](http://robot.obolibrary.org/): A command line tool to automate ontology workflows. It includes commands that can be used manually or integrated in automated processes to develop and release ontologies.
 - [Protégé](https://protege.stanford.edu/): An ontology editing environment for OWL ontologies. It allows developers to visualize the ontology hierarchy, add and edit ontology terms, reason over the ontology, and more.
 - [Onto-Animals](http://www.hegroup.org/ontozoo/): Tools to extract external ontology terms, compare ontologies, edit ontology terms, query and visualize ontologies, and more.
-- [VOCOL](https://vocol.iais.fraunhofer.de/): An integrated environment for collaborative vocabulary development
+- [VOCOL](https://github.com/vocol/vocol): An integrated environment for collaborative vocabulary development
 - [Karma Data Integration](http://usc-isi-i2.github.io/karma/): A data integration tool
 - [Ontofox](http://ontofox.hegroup.org/): An ontology term and relation extraction and reuse tool
 - [Ubergraph](https://github.com/INCATools/ubergraph): A sparql endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized