Add curation_rule to SSSOM (#258)

Fixes #166

- [X] `docs/` have been added/updated if necessary
- [X] `make test` has been run locally
- [X] tests have been added/updated (if applicable)
- [ ]

The need for representing specific curation rules is everywhere, see
#166. It will be very difficult, if not impossible, to standardise
curation rules, so I would advocate we leave this totally open for now.
Representing the rules as a resource basically makes them an open ended
enum - which gives us more flexibility for adding structure later.
@saubin78 suggested to create a class "MappingRule" and have curation
rules being instances of mapping rules.

We also should decide reasonably soon if we want to rename curation rule
into mapping rule altogether, if we agree with @saubin78 assertion in
#166 that computational rules can also be curation rules (I think that's
fair!).

examples/schema/curation_rule.sssom.tsv

@@ -0,0 +1,14 @@
+#curie_map:
+#  HP: http://purl.obolibrary.org/obo/HP_
+#  MP: http://purl.obolibrary.org/obo/MP_
+#  orcid: https://orcid.org/
+#  DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/
+#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule.sssom.tsv
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#creator_id: orcid:0000-0002-7356-1779
+#mapping_provider: "https://w3id.org/sssom/core_team"
+#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
+subject_id	predicate_id	object_id	mapping_justification	curation_rule	see_also
+HP:0009124	skos:exactMatch	MP:0000003	semapv:ManualMappingCuration	DISEASE_MAPPING_COMMONS_RULES:MPR2	https://github.com/mapping-commons/disease-mappings/issues/16
+HP:0008551	skos:exactMatch	MP:0000018	semapv:ManualMappingCuration	DISEASE_MAPPING_COMMONS_RULES:MPR3	https://github.com/mapping-commons/disease-mappings/issues/16
+HP:0000411	skos:exactMatch	MP:0000021	semapv:ManualMappingCuration	DISEASE_MAPPING_COMMONS_RULES:MPR3	https://github.com/mapping-commons/disease-mappings/issues/16

examples/schema/curation_rule_text.sssom.tsv

@@ -0,0 +1,14 @@
+#curie_map:
+#  HP: http://purl.obolibrary.org/obo/HP_
+#  MP: http://purl.obolibrary.org/obo/MP_
+#  orcid: https://orcid.org/
+#  DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/
+#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule_text.sssom.tsv
+#license: "https://creativecommons.org/publicdomain/zero/1.0/"
+#creator_id: orcid:0000-0002-7356-1779
+#mapping_provider: "https://w3id.org/sssom/core_team"
+#comment: This is an example file for the SSSOM for illustration only. Its contents are entirely fabricated.
+subject_id	predicate_id	object_id	mapping_justification	curation_rule_text	see_also
+HP:0009124	skos:exactMatch	MP:0000003	semapv:ManualMappingCuration	The two phenotypes inhere in homologous structures and exhibit the same phenotypic quality	https://github.com/mapping-commons/disease-mappings/issues/16
+HP:0008551	skos:exactMatch	MP:0000018	semapv:ManualMappingCuration	The two phenotypes inhere in homologous structures and exhibit the same phenotypic quality	https://github.com/mapping-commons/disease-mappings/issues/16
+HP:0000411	skos:exactMatch	MP:0000021	semapv:ManualMappingCuration	The two phenotypes are associated with the exact same set of diseases	https://github.com/mapping-commons/disease-mappings/issues/16

examples/schema/curation_rule_text2.sssom.tsv

@@ -0,0 +1,18 @@
+#curie_map:
+#  WTO: http://purl.obolibrary.org/obo/WTO_
+#  CO321: "http://www.cropontology.org/rdf/CO_321:"
+#  ror: https://ror.org/
+#mapping_set_id: https://w3id.org/sssom/commons/examples/curation_rule_text2.sssom.tsv
+#license: "https://www.etalab.gouv.fr/licence-ouverte-open-licence/"
+#comment: This is an example file for the SSSOM for illustration only. This example was extracted from a real mapping set where the subject source (WTO) is an ontology used to annotate text (e.g. scientific literature) and the object source (CO321) is an ontology used to annotate the traits evaluated from observational data. The objective of the alignment is to allow information retrieval from both textual and experimental phenotypic dataset.
+#creator_id: ror:02kvxyf05
+#creator_label: "INRAE"
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	curation_rule_text	comment
+WTO:0000304	cold resistance	skos:closeMatch	CO321:0000080	Cold tolerance	semapv:ManualMappingCuration	Rule 4: We consider that "tolerance" and "resistance" are almost equivalent when applied to abiotic environmental conditions. 
+WTO:0000450	aluminium toxicity	skos:closeMatch	CO321:0000079	Aluminum tolerance	semapv:ManualMappingCuration	Rule 3: We consider that the user of the information retrieval function interested in plant traits related to metal toxicity  (WTO) also wants to retrieve observational data measuring the plant tolerance to the same metal (CO_321). The rule metal + toxicity (WTO) <-> metal + tolerance  (CO321) is valid for any kind of metal.
+WTO:0000065	anther extrusion	skos:exactMatch	CO321:0000982	Anther extrusion	semapv:ManualMappingCuration		
+WTO:0000296	aphid resistance	skos:closeMatch	CO321:0000085	Aphid damage	semapv:ManualMappingCuration	Rule 2: We consider that the user of the information retrieval function interested in plant traits related to damages caused by some animal,  insect, nematode, etc. also wants to retrieve observational data mentioning resistance to the same living organism.
+WTO:0000281	Armyworm resistance	skos:closeMatch	CO321:0000086	Armyworm damage	semapv:ManualMappingCuration	Rule 2: We consider that the user of the information retrieval function interested in plant traits related to damages caused by some animal,  insect, nematode, etc. also wants to retrieve observational data mentioning resistance to the same living organism.
+WTO:0000125	awn color	skos:exactMatch	CO321:0000960	Awn color	semapv:ManualMappingCuration		
+WTO:0000126	awn length	skos:exactMatch	CO321:0000026	Awn length	semapv:ManualMappingCuration		
+WTO:0000452	bacterial leaf blight resistance	skos:closeMatch	CO321:0000932	Bacterial leaf blight severity	semapv:ManualMappingCuration	Rule 1.3: We consider that the user of the information retrieval function, given a pathogen or a disease, would like to retrieve all data, independently of the way the affection is observed. In observational data, a severity score is represented by two digits representing the vertical disease progress and an estimate of severity. The capacity of resistance to a disease would be deduced from the severity of this one on the plant.

src/sssom_schema/schema/sssom_schema.yaml

@@ -446,6 +446,29 @@ slots:
     examples:
       - value: semapv:Stemming
       - value: semapv:StopWordRemoval
+  curation_rule:
+    description: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. 
+      Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation
+      rule is captured as a resource rather than a string, which enables higher levels of transparency and sharing across mapping sets.
+      The URI representation of the curation rule is expected to be a resolvable identifier which provides details about the nature of the curation rule.
+    range: EntityReference
+    multivalued: true
+    see_also: 
+      - https://github.com/mapping-commons/sssom/issues/166
+      - https://github.com/mapping-commons/sssom/pull/258
+      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule.sssom.tsv
+  curation_rule_text:
+    description: A curation rule is a (potentially) complex condition executed by an agent that led to the establishment of a mapping. 
+      Curation rules often involve complex domain-specific considerations, which are hard to capture in an automated fashion. The curation
+      rule should be captured as a resource (entity reference) rather than a string (see curation_rule element), which enables higher levels of transparency and sharing across mapping sets.
+      The textual representation of curation rule is intended to be used in cases where (1) the creation of a resource is not practical from the
+      perspective of the mapping_provider and (2) as an additional piece of metadata to augment the curation_rule element with a human readable text.
+    range: string
+    multivalued: true
+    see_also:
+      - https://github.com/mapping-commons/sssom/issues/166
+      - https://github.com/mapping-commons/sssom/pull/258
+      - https://github.com/mapping-commons/sssom/blob/master/examples/schema/curation_rule_text.sssom.tsv
   semantic_similarity_score:
     description: A score between 0 and 1 to denote the semantic similarity, where
       1 denotes equivalence.
@@ -539,6 +562,8 @@ classes:
     - mapping_tool_version
     - mapping_date
     - confidence
+    - curation_rule
+    - curation_rule_text
     - subject_match_field
     - object_match_field
     - match_string