From 7ddcf6215d6bc9b09e29dd4adef00def3295ce7c Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 16 Feb 2023 16:28:01 +0200 Subject: [PATCH 1/8] Update sssom_schema.yaml --- src/sssom_schema/schema/sssom_schema.yaml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 2197ef58..d51b2787 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -423,6 +423,14 @@ 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 semantic_similarity_score: description: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence. @@ -516,6 +524,7 @@ classes: - mapping_tool_version - mapping_date - confidence + - curation_rule - subject_match_field - object_match_field - match_string From 097a6bca1c562c56192b407611487702e78a6196 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Fri, 3 Mar 2023 17:11:05 +0200 Subject: [PATCH 2/8] Update sssom_schema.yaml --- src/sssom_schema/schema/sssom_schema.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 8c69674a..4a43309f 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -445,6 +445,15 @@ slots: range: EntityReference multivalued: true see_also: https://github.com/mapping-commons/sssom/issues/166 + 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 semantic_similarity_score: description: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence. @@ -539,6 +548,7 @@ classes: - mapping_date - confidence - curation_rule + - curation_rule_text - subject_match_field - object_match_field - match_string From 0d3ccec2f0f799b436c66b8ba65fb5fbd8f895df Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 14 Mar 2023 12:41:32 +0200 Subject: [PATCH 3/8] Update sssom_schema.yaml --- src/sssom_schema/schema/sssom_schema.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index 4a43309f..d3d1eaea 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -444,7 +444,9 @@ slots: 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 + see_also: + - https://github.com/mapping-commons/sssom/issues/166 + - https://github.com/mapping-commons/sssom/pull/258 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 @@ -453,7 +455,9 @@ slots: 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 + see_also: + - https://github.com/mapping-commons/sssom/issues/166 + - https://github.com/mapping-commons/sssom/pull/258 semantic_similarity_score: description: A score between 0 and 1 to denote the semantic similarity, where 1 denotes equivalence. From bbf41889ce1680d1eca574cd0e6fff57ba596c0c Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 14 Mar 2023 13:13:41 +0200 Subject: [PATCH 4/8] Create curation_rule.sssom.tsv --- examples/schema/curation_rule.sssom.tsv | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 examples/schema/curation_rule.sssom.tsv diff --git a/examples/schema/curation_rule.sssom.tsv b/examples/schema/curation_rule.sssom.tsv new file mode 100644 index 00000000..37fcadfa --- /dev/null +++ b/examples/schema/curation_rule.sssom.tsv @@ -0,0 +1,13 @@ +#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/ +#creator_id: orcid:0000-0002-7356-1779 +#license: "https://creativecommons.org/publicdomain/zero/1.0/" +#mapping_provider: "https://w3id.org/sssom/core_team" +#comment: This is an example file for the SSSOM +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 From 5c6b622ff76e8fd321bccfa35a6f99007251dd77 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 14 Mar 2023 13:16:02 +0200 Subject: [PATCH 5/8] Add more examples --- examples/schema/curation_rule.sssom.tsv | 2 +- examples/schema/curation_rule_text.sssom.tsv | 13 +++++++++++++ 2 files changed, 14 insertions(+), 1 deletion(-) create mode 100644 examples/schema/curation_rule_text.sssom.tsv diff --git a/examples/schema/curation_rule.sssom.tsv b/examples/schema/curation_rule.sssom.tsv index 37fcadfa..63789bba 100644 --- a/examples/schema/curation_rule.sssom.tsv +++ b/examples/schema/curation_rule.sssom.tsv @@ -6,7 +6,7 @@ #creator_id: orcid:0000-0002-7356-1779 #license: "https://creativecommons.org/publicdomain/zero/1.0/" #mapping_provider: "https://w3id.org/sssom/core_team" -#comment: This is an example file for the SSSOM +#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 diff --git a/examples/schema/curation_rule_text.sssom.tsv b/examples/schema/curation_rule_text.sssom.tsv new file mode 100644 index 00000000..4911b8e2 --- /dev/null +++ b/examples/schema/curation_rule_text.sssom.tsv @@ -0,0 +1,13 @@ +#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/ +#creator_id: orcid:0000-0002-7356-1779 +#license: "https://creativecommons.org/publicdomain/zero/1.0/" +#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 From c8c97eead6a6e51ac13a58c84549d555204a6592 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Tue, 14 Mar 2023 13:21:05 +0200 Subject: [PATCH 6/8] adding link to example files to schema --- src/sssom_schema/schema/sssom_schema.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/sssom_schema/schema/sssom_schema.yaml b/src/sssom_schema/schema/sssom_schema.yaml index d3d1eaea..4cd7e627 100644 --- a/src/sssom_schema/schema/sssom_schema.yaml +++ b/src/sssom_schema/schema/sssom_schema.yaml @@ -447,6 +447,7 @@ slots: 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 @@ -458,6 +459,7 @@ slots: 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. From 9243fa95e339e6eb794238b48bf2a16ce2605b9e Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 16 Mar 2023 13:09:22 +0200 Subject: [PATCH 7/8] Update examples --- examples/schema/curation_rule.sssom.tsv | 3 ++- examples/schema/curation_rule_text.sssom.tsv | 3 ++- examples/schema/curation_rule_text2.sssom.tsv | 16 ++++++++++++++++ 3 files changed, 20 insertions(+), 2 deletions(-) create mode 100644 examples/schema/curation_rule_text2.sssom.tsv diff --git a/examples/schema/curation_rule.sssom.tsv b/examples/schema/curation_rule.sssom.tsv index 63789bba..3e9d7b7e 100644 --- a/examples/schema/curation_rule.sssom.tsv +++ b/examples/schema/curation_rule.sssom.tsv @@ -3,8 +3,9 @@ # MP: http://purl.obolibrary.org/obo/MP_ # orcid: https://orcid.org/ # DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/ -#creator_id: orcid:0000-0002-7356-1779 +#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 diff --git a/examples/schema/curation_rule_text.sssom.tsv b/examples/schema/curation_rule_text.sssom.tsv index 4911b8e2..2a2fc60f 100644 --- a/examples/schema/curation_rule_text.sssom.tsv +++ b/examples/schema/curation_rule_text.sssom.tsv @@ -3,8 +3,9 @@ # MP: http://purl.obolibrary.org/obo/MP_ # orcid: https://orcid.org/ # DISEASE_MAPPING_COMMONS_RULES: https://w3id.org/sssom/commons/disease/curation-rules/ -#creator_id: orcid:0000-0002-7356-1779 +#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 diff --git a/examples/schema/curation_rule_text2.sssom.tsv b/examples/schema/curation_rule_text2.sssom.tsv new file mode 100644 index 00000000..79a2343d --- /dev/null +++ b/examples/schema/curation_rule_text2.sssom.tsv @@ -0,0 +1,16 @@ +#curie_map: +# wto: "http://purl.obolibrary.org/obo/"" +# CO321: "http://www.cropontology.org/rdf/CO_321:" +#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: "https://ror.org/02kvxyf05" +#creator_label: "INRAE" +subject_id subject_label predicate_id object_id object_label mapping_justification curation_rule_text comment +wto:WTO_0000304 cold resistance skos:closeMatch CO_321:0000080 Cold tolerance semapv:ManualMappingCuration Rule 4: We consider that "tolerance" and "resistance" are almost equivalent when applied to abiotic environmental conditions. +wto: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:WTO_0000065 anther extrusion skos:exactMatch CO321:0000982 Anther extrusion semapv:ManualMappingCuration +wto: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: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:WTO_0000125 awn color skos:exactMatch CO321:0000960 Awn color semapv:ManualMappingCuration +wto:WTO_0000126 awn length skos:exactMatch CO321:0000026 Awn length semapv:ManualMappingCuration +wto: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. \ No newline at end of file From a301cfe21dd8f3e5f1490e13f3d7e228edabbba0 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 16 Mar 2023 14:16:54 +0200 Subject: [PATCH 8/8] Update curation_rule_text2.sssom.tsv --- examples/schema/curation_rule_text2.sssom.tsv | 22 ++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/examples/schema/curation_rule_text2.sssom.tsv b/examples/schema/curation_rule_text2.sssom.tsv index 79a2343d..3c5777ea 100644 --- a/examples/schema/curation_rule_text2.sssom.tsv +++ b/examples/schema/curation_rule_text2.sssom.tsv @@ -1,16 +1,18 @@ #curie_map: -# wto: "http://purl.obolibrary.org/obo/"" +# 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: "https://ror.org/02kvxyf05" +#creator_id: ror:02kvxyf05 #creator_label: "INRAE" subject_id subject_label predicate_id object_id object_label mapping_justification curation_rule_text comment -wto:WTO_0000304 cold resistance skos:closeMatch CO_321:0000080 Cold tolerance semapv:ManualMappingCuration Rule 4: We consider that "tolerance" and "resistance" are almost equivalent when applied to abiotic environmental conditions. -wto: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:WTO_0000065 anther extrusion skos:exactMatch CO321:0000982 Anther extrusion semapv:ManualMappingCuration -wto: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: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:WTO_0000125 awn color skos:exactMatch CO321:0000960 Awn color semapv:ManualMappingCuration -wto:WTO_0000126 awn length skos:exactMatch CO321:0000026 Awn length semapv:ManualMappingCuration -wto: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. \ No newline at end of file +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. \ No newline at end of file