Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Minor fix to the “overview” document regarding the TSV format #284

Merged
merged 2 commits into from
Jun 11, 2023
Merged

Minor fix to the “overview” document regarding the TSV format #284

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
87ec71f
Do not allow `curie_map` to be a link to a curie map.
gouttegd Jun 10, 2023
14d8048
Fix discrepancy regarding the naming of the external YAML file.
gouttegd Jun 10, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions src/docs/spec.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -353,14 +353,14 @@ SubClassOf(Annotation(sssom:creator_id <https://orcid.org/0000-0002-7356-1779>)

All SSSOM metadata elements labelled with L in the metadata table are permissible as column names in the TSV. List elements (such as creator) are "|"-separated. The columns MUST be sorted according to the order as they appear in the [SSSOM metadata](https://mapping-commons.github.io/sssom/Mapping/). For example, the first columns of a mapping set TSV should always be, in that order: subject_id, predicate_id, object_id, mapping_justification, if labels are not included; if they are included, the order should be: subject_id, subject_label, predicate_id, predicate_label, object_id, object_label, mapping_justification. For easier review of diffs, for example git diff or unix diff, we recommend to serialise the TSV by a fixed row order, sorted column by column from left to right.

Metadata about a set of mappings can be supplied as part of the mappings (embedded mode) and as a simple yaml file alongside the primary mapping file. Note that for the TSV, it will be required to supply a valid curie map that allows the unambiguous interpretation of CURIEs. A curie map is supplied after a `curie_map:` parameter in the yaml file. The value can be either a dictionary of CURIE->URLPREFIX pairs or a link to a valid curie map of the same shape.
Metadata about a set of mappings can be supplied as part of the mappings (embedded mode) and as a simple yaml file alongside the primary mapping file. Note that for the TSV, it will be required to supply a valid curie map that allows the unambiguous interpretation of CURIEs. A curie map is supplied after a `curie_map:` parameter in the yaml file. The value is a dictionary of CURIE->URLPREFIX pairs.

Note that only metadata elements permissible in a global context (G, or L/G) can be used in the metadata-file.

We recommend to use the following *filename conventions* for SSSOM metadatafiles:

- TSV files should have the extension `.sssom.tsv`, for example: `mp-hp-exact-0.0.1.sssom.tsv`.
- External yaml metadata files should have the extension `.sssom.yml`, for example `mp-hp-exact-0.0.1.sssom.tsv`
- External yaml metadata files should have the extension `.sssom.yml`, for example `mp-hp-exact-0.0.1.sssom.yml`

Example ([download](https://raw.githubusercontent.com/mapping-commons/sssom/master/examples/external/mp-hp-exact-0.0.1.sssom.yml)):

Expand All @@ -376,7 +376,7 @@ mapping_provider: "http://purl.obolibrary.org/obo/upheno.owl"

#### External mode

In external mode, the mapping set metadata is supplied by a separate YAML file having the same base-name of the mapping file, with the extension `-meta.yml`. By default, tools will look for the file of that name in the same directory as the the mapping set table.
In external mode, the mapping set metadata is supplied by a separate YAML file having the same base-name of the mapping file, with the extension `.sssom.yml`. By default, tools will look for the file of that name in the same directory as the the mapping set table.

Example ([download](https://raw.githubusercontent.com/mapping-commons/sssom/master/examples/external/mp-hp-exact-0.0.1.sssom.tsv)):

Expand Down