matentzn
commented
4 years ago Thanks a ton @NuriaQueralt Great idea! If you find anything missing in SSSOM, we can gladly add it in; Do you have someone handy that could do a comparison perhaps?
Open NuriaQueralt opened 4 years ago
matentzn
commented
4 years ago Thanks a ton @NuriaQueralt Great idea! If you find anything missing in SSSOM, we can gladly add it in; Do you have someone handy that could do a comparison perhaps?
NuriaQueralt
commented
4 years ago Myself! :)
matentzn
commented
3 years ago @NuriaQueralt :) Hey. I am now starting to align your nice metadata schema with SSSOM, but I need a bit of help with that I think.. Would you be happy to set up a meeting to go through some of the issues? In the meantime, is there any more documentation on the Fields you mention in Table 1 of your paper?
matentzn
commented
3 years ago And perhaps and example dataset.
NuriaQueralt
commented
3 years ago Hi @matentzn thank you for touching base on that! Set up a meeting sounds good. How about the week from Jul 19th?
matentzn
commented
3 years ago matentzn
commented
3 years ago Thanks for all the input @NuriaQueralt
This is the current state:
| Status | Biohackathon 2015 Attribute | SSSOM element | Source | Comment | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| done | Identifier (IRI) | mapping_set_id | FAIR | |||||||||
| done | Title | mapping_set_title | Open PHACTS | |||||||||
| done | Description | mapping_set_description | Open PHACTS | |||||||||
| done | License | license | Open PHACTS | |||||||||
| done | Type of Subject | subject_category | Open PHACTS | |||||||||
| done | Type of Object | object_category | Open PHACTS | |||||||||
| done | Link to Subject dataset metadata | subject_source, subject_source_version | Open PHACTS | |||||||||
| done | Link to Object dataset metadata | object_source, subject_source_version | Open PHACTS | |||||||||
| done | Mapping relationship | predicated_id; | Open PHACTS | |||||||||
| done | Creator-who | creator_id | Open PHACTS | |||||||||
| done | Creator-when | mapping_date | ||||||||||
| done | Concept overlap value (n:m) | mapping_cardinality | BioHackathon 2015 | |||||||||
| done | Provenance/source of mapping (ontology/dictionary/database + version) | mapping_provider | BioHackathon 2015 | |||||||||
| done | Mapping version | mapping_set_version | BioHackathon 2015 | |||||||||
| issue | Issued | mapping_set_issue_date | Open PHACTS | |||||||||
| issue | Link to mapping file | mapping_set_data | Open PHACTS | |||||||||
| issue | Version of mapping tool | mapping_tool_version | Open PHACTS | |||||||||
| issue | Curation state | new one? | ORDO | |||||||||
| issue | Mapping previous version | new term? | BioHackathon 2015 | |||||||||
| issue | Ontology version | mapping_provider | BioHackathon 2015 | |||||||||
| issue | Sustainability (code development environment) | BioHackathon 2015 | ||||||||||
| issue | Link to mapping tool metadata | mapping_tool_version | BioHackathon 2015 | |||||||||
| issue | Authorship-who | author_id | Open PHACTS | |||||||||
| nico | Authorship-when | Open PHACTS | Make ticket to discuss with the rest of the community. Legal term - when did the agend became an author | |||||||||
| nico | Evidence (PMID, Web, EHR..) | BioHackathon 2015 | found in a paper, determined by NLP, etc etc | |||||||||
| issue | Curation author | ORDO | ||||||||||
| nico | Curation date | ORDO | ||||||||||
| issue | Publisher | mapping_set_publisher | Open PHACTS | dcterms:publisher ===>The publisher for a dataset is the organisation that is responsible for the creation and maintenance for the dataset. This predicate should point to the web page for the organisation. For example, the publisher of the ChemSpider dataset is the Royal Society of Chemistry and the value for this property is http://www.rsc.org/. Ideally the publisher's page should be marked up with RDFa so that it is machine processable. | ||||||||
| remove | Type of Mapping | g2p, d2p, d2d; | Open PHACTS | REMOVE. mapping as a class, when the mapping is represented as an entity such as in DisGeNET and OBAN, not as a relationship. Mapping relationships such as |
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| issue | Mapping justification: Declare the notion of equivalence using bdb:linksetJustification with one of the reasons given in Appendix B.2. | eg: :linkset_metadata_file_uri bdb:linksetJustification sio:SIO_010043 ; | Open PHACTS | Justifications such as |
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| nico | Assertion method: Declare whether the links have been computer generated or manually verified using bdb:assertionMethod with one of the assertion levels given in Appendix B.4. | eg: :linkset_metadata_file_uri bdb:assertionMethod eco:ECO_0000218 . | Open PHACTS | Declare whether the links have been computer generated or manually verified using bdb:assertionMethod with one of the assertion levels given in: http://www.openphacts.org/specs/2013/WD-datadesc-20130912/#appendix-assertion-methods | ||||||||
| remove | Assertion value (exact, ntbt, …) | ORDO | The ORDO ontology in Orphanet models mappings with axioms where it includes this value next to the assertion method URI, e.g. |
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| remove | Mapping directionality | ? | OBAN | REMOVE. This only makes sense if the mapping is a class and 'subject' and 'object' are not specified. | ||||||||
| issue | Mapping state (active, obsolete, other) | mapping_state | BioHackathon 2015 | |||||||||
| remove | Curation justification | BioHackathon 2015 | REMOVABLE. Data property to link to a text sentence, extracted by the curator or a text mining system from the source of evidence, that adds a human readable text that supports its decision. Usually the sentence 'read' from the PubMed ID source of evidence. Pros: it is useful for human reasoning. Cons: It is not best practices because it is neither machine readable nor for automated reasoning (computable). | |||||||||
| remove | Link to the linkset metadata | BioHackathon 2015 | REMOVABLE. In case metadata description and actual mappings are in different files, mappings should link to its metadata description file. | |||||||||
| remove | Link to the ontology metadata | mapping_provider_metadata | BioHackathon 2015 | REMOVE. I think it is redundant if SSSOM already has a predicate like 'mapping provider metadata' |
We will get back to this in the next iteration.
Dear all,
During the BioHackathon 2015, we proposed metadata for both ontologies and mappings within ontologies, see section Ontology metadata mapping. in [1]. I've looked through the SSSOM scheme and I detected some overlap. It'd be good to check the non-overlapping ones to evaluate to be added to SSSOM? Many thanks in advance.
[1] F1000 BH15 paper