Merge branch 'master' into issue78-tracker

.github/ISSUE_TEMPLATE/new_sssom_element.md

@@ -22,4 +22,26 @@ xsd:string
 **Description**
 (Provide a human-readable description that clarifies the intended use of the metadata element.)
 
-Example description.
+Example description.
+
+**Complete example to a SSSOM file with this element**
+(This example can be given as a markdown table or a linked SSSOM file, feel free to edit the markdown table below)
+
+```
+# curie_map:
+#   HP: http://purl.obolibrary.org/obo/FBbt_
+#   MP: http://purl.obolibrary.org/obo/UBERON_
+#   owl: http://www.w3.org/2002/07/owl#
+#   rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+#   rdfs: http://www.w3.org/2000/01/rdf-schema#
+#   semapv: https://w3id.org/semapv/vocab/
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   sssom: https://w3id.org/sssom/
+# license: https://w3id.org/sssom/license/unspecified
+# mapping_set_id: https://w3id.org/sssom/mappings/ac9e1878-73f4-4767-8402-a6c40e1b0835
+```
+
+| subject_id	| predicate_id	  | object_id	  | mapping_justification   | element_id_example	| 
+| ----------- | --------------- | ----------- | ----------------------- | ------------------- |
+| HP:0009124	| skos:exactMatch	| MP:0000003	| semapv:LexicalMatching	| YOUR EXAMPLE VALUE	| 
+| HP:0008551	| skos:exactMatch	| MP:0000018	| semapv:LexicalMatching	| YOUR EXAMPLE VALUE	|

.github/pull_request_template.md

@@ -3,6 +3,13 @@ Resolves [#ISSUE, #ISSUE]
 - [ ] `docs/` have been added/updated if necessary
 - [ ] `make test` has been run locally
 - [ ] tests have been added/updated (if applicable)
-- [ ] [CHANGELOG.md](https://github.com/mapping-commons/sssom/blob/0.9.0/CHANGELOG.md) has been updated.
+- [ ] [CHANGELOG.md](https://github.com/mapping-commons/sssom/blob/master/CHANGELOG.md) has been updated.
 
-[Description, mentioning at least relevant #ISSUE and how it was addressed. A bulleted list of all changes performed by the PR is is helpful.]
+If you are proposing a change to the SSSOM metadata model, you must 
+
+- [ ] provide a full, working and valid example in `examples/`
+- [ ] provide a link to the related GitHub issue in the `see_also` field of the linkml model
+- [ ] provide a link to a valid example in the `see_also` field of the linkml model
+
+
+[Add a description, mentioning at least relevant #ISSUE and how it was addressed. A bulleted list of all changes performed by the PR is is helpful.]

.github/workflows/qc.yml

@@ -0,0 +1,31 @@
+# Basic ODK workflow
+
+name: CI
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  sssom_validation:
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.4
+    steps:
+      - name: Install latest SSSOM
+        env:
+          DEFAULT_BRANCH: master
+        run: pip install --upgrade pip && pip install -U sssom sssom-schema
+      - uses: actions/checkout@v2
+      - name: Run Mapping QC checks
+        env:
+          DEFAULT_BRANCH: master
+        run: make validate_mappings
+

CHANGELOG.md

@@ -1,8 +1,37 @@
 # Changelog for SSSOM
 
-## SSSOM version 1.0
+## SSSOM version 0.13.0
 
-- TBD
+- The necessity of the "canonical column ordering" was downgraded from MUST to SHOULD (https://github.com/mapping-commons/sssom/pull/285)
+- Documents clearly that built-in prefixes MUST NOT be redefined (https://github.com/mapping-commons/sssom/pull/285)
+
+## SSSOM version 0.11.0
+
+- see https://github.com/mapping-commons/sssom/releases/tag/0.11.0
+
+### Summary
+
+#### New elements:
+- `mapping_set_title` to capture a human readable title for a mapping set
+- `registry_title` and `registry_description` to capture the human readable title and description of an SSSOM mapping set registry
+- `curation_rule` to capture a (potentially) complex (set of) condition(s) executed by an agent (usually human) that led to the establishment of a mapping. 
+
+#### Updated elements:
+- Adding mapping_source slot to Mapping by @matentzn in #230
+- Improve documentation for `subject_category` and `object_category` elements
+
+#### Documentation
+- Compiled a list of all SSSOM talks: https://mapping-commons.github.io/sssom/presentations/
+- Document chaining rules: https://mapping-commons.github.io/sssom/chaining_rules/
+
+#### Quality control and Technical infrastructure
+
+- Make adding a concrete SSSOM example part of the new element request
+- Adding QC checks for example SSSOM files hosted in the repo
+
+## SSSOM version 0.10.1
+
+- see https://github.com/mapping-commons/sssom/releases/tag/0.10.1
 
 ## SSSOM version 0.9.4
 

Makefile

@@ -40,7 +40,7 @@ install:
 	poetry install
 .PHONY: install
 
-all: gen-project gendoc gen-excel
+all: gen-project gendoc gen-excel get-context
 %.yaml: gen-project
 deploy: all mkd-gh-deploy
 
@@ -57,6 +57,10 @@ check-config:
 convert-examples-to-%:
 	$(patsubst %, $(RUN) linkml-convert  % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell find src/data/examples -name "*.yaml")) 
 
+get-context:
+	mkdir -p $(SRC)/$(SCHEMA_NAME)/context
+	cp $(DEST)/jsonld/* $(SRC)/$(SCHEMA_NAME)/context
+
 examples/%.yaml: src/data/examples/%.yaml
 	$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
 examples/%.json: src/data/examples/%.yaml

README.md

@@ -58,3 +58,5 @@ Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush,
     eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac035/43832024/baac035.pdf},
 }
 ```
+
+A [second report with updates since the primary SSSOM publication](https://ceur-ws.org/Vol-3324/om2022_LTpaper6.pdf) above was published as part of the proceedings of the Ontology Matching Workshop 2022.

examples/embedded/foodie-inc-2022-05-01.sssom.tsv

@@ -1,20 +1,26 @@
-# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
+# comment: We could map to FOODON:00004187 instead which more specifically refers to
+#   'raw' Pink apples. Decided against to be consistent with other mapping choices.
+# curie_map:
+#   FOODON: http://purl.obolibrary.org/obo/FOODON_
+#   KF_FOOD: https://kewl-foodie.inc/food/
+#   orcid: https://orcid.org/
+#   owl: http://www.w3.org/2002/07/owl#
+#   rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns#
+#   rdfs: http://www.w3.org/2000/01/rdf-schema#
+#   semapv: https://w3id.org/semapv/vocab/
+#   skos: http://www.w3.org/2004/02/skos/core#
+#   sssom: https://w3id.org/sssom/
+#   wikidata: https://www.wikidata.org/wiki/
 # license: https://creativecommons.org/licenses/by/4.0/
 # mapping_date: '2022-05-02'
 # mapping_set_description: Manually curated alignment of KEWL FOODIE INC internal food
 #   and nutrition database with Food Ontology (FOODON). Intended to be used for ontological
 #   analysis and grouping of KEWL FOODIE INC related data.
+# mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
 # mapping_set_version: '2022-05-01'
 # object_source: wikidata:Q55118395
 # object_source_version: http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl
 # subject_source: KF_FOOD:DB
-# comment: We could map to FOODON:00004187 instead which more specifically refers to
-#   'raw' Pink apples. Decided against to be consistent with other mapping choices.
-# curie_map:
-#   FOODON: http://purl.obolibrary.org/obo/FOODON_
-#   KF_FOOD: https://kewl-foodie.inc/food/
-#   skos: http://www.w3.org/2004/02/skos/core#
-#   sssom: https://w3id.org/sssom/
 subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	author_id	object_source_version	mapping_date	confidence	comment
 KF_FOOD:F001	apple	skos:exactMatch	FOODON:00002473	apple (whole)	semapv:ManualMappingCuration	orcid:0000-0002-7356-1779	http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl	2022-05-02	0.95	"We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist."
 KF_FOOD:F002	gala	skos:exactMatch	FOODON:00003348	Gala apple (whole)	semapv:ManualMappingCuration	orcid:0000-0002-7356-1779	http://purl.obolibrary.org/obo/foodon/releases/2022-02-01/foodon.owl	2022-05-02	1.0