INCATools / INCATools/boomer

Output sssom mapping files rather than (just) owl

Open
#293 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
Scala
Stars
37
Forks
2
PR merge metrics
No merged PRs in 30d

Description

For working with boomer more seemlessly, it would be great if it could output the results as a table:

```
mapping_set_id: https://w3id.org/boomer/s8169763872632786387263
license: https://creativecommons.org/publicdomain/zero/1.0/
curie_map:
UBERON: http...
FMA: http...
```
| subject_id | subject_label | predicate_id | object_id | object_label | confidence | mapping_justification |
| ---------- | ---------- | ---------- | ---------- | ---------- | ---------- | ---------- |
| UBERON:123 | heart | skos:exactMatch | FMA:321 | heart | 0.9 | semapv:UnspecifiedMatching |
| UBERON:123 | soul | skos:exactMatch | FMA:321 | human soul | 0.9 | semapv:UnspecifiedMatching |

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by locating the code that currently writes OWL output and trace how mapping results are represented before serialization. Compare the requested metadata and table columns with the existing output path; done means boomer can emit the requested SSSOM-style mapping file in addition to OWL, with tests covering the format.

Written by the indexing model from the issue text.

Assessment

Tech stack
scala
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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