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Add curation_rule to SSSOM #258
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Update sssom_schema.yaml
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Merge branch 'master' into issue166-curationrule
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Merge branch 'master' into issue166-curationrule
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Create curation_rule.sssom.tsv
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Add more examples
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adding link to example files to schema
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#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 |
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#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 |
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#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. |
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i want to go as far as saying that we should enforce that the examples given are REAL and not fabricated... Or am I asking too much that people should explain in detail and give real concrete use cases before SSSOM gets polluted with lots of indecipherable fields?
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Further, https://w3id.org/sssom/commons/disease/curation-rules/MPR2 does not resolve to anything, therefore I can not understand what this means, and can not review the merits of this field based on this example
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By fabricated I mean: this is not to be used / maintained for any practical purposes. I am totally out of steam on this one - we can push for incremental improvements moving forward. This example has real curation rules, I just didn't apply them to real data..
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This is what I tried to explain in our last call - PURLs should, but don't have to, resolve to something. Its not part of SSSOM to prescribe what goes in these curation rules. Different communities will decide to create shareable representations, and they will decide to provide resolveable resources and examples. When you review a PR of a mapping set for use, you can, in your organisation, apply whatever quality thresholds you want during the review. On SSSOM metadata level we just say: there is an element to represent curation rules, this is how you do it.
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:( I am sorry that my feedback has exhausted you.
You and I both know what this means :p
How can we move forwards so the burden of making good, actionable improvements to SSSOM is distributed from you to community members who are requesting them? E.g., improving the new field request template, adding more CI/CD is a great start.
@saubin78 for a start, can you help alleviate some of this burden? Can you help provide actionable examples of how this might work (e.g., improve the example files Nico made to actually be meaningful examples)? Then, Nico won't feel so much burden from me giving important (but ultimately difficult to address) feedback in addition to the project-based pressure to just "get this done" that if done prematurely, could erode trust and sustainability of SSSOM (and more burn out)?
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I don't disagree with this. But I think it's reasonable to ask that people who are making proposals of new fields to go above and beyond the minimum requirements of PURLs to give context to these fields for the purpose of an example. As it is, without a herculean effort of reading through meandering GitHub issue conversations and documentation in various places, it's really not obvious to understand what's going on here. If we can't agree on this, can we at least agree that there should be a detailed explanation in the preamble of the SSSOM document explaining what the new predicates are supposed to be for?