sssom

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Based on https://docs.google.com/document/d/1qstv4teykJ8yaS8zpHjotFNfZYPfaghU-Yo0dkCia-Y/edit#heading=h.lfpgx1ffstyp

matentzn

**Element id (e.g. creator_id, mapping_tool_version):** (Must be lower case and contain only letters and underscores.) ``` sparql_expansion ``` **Value data type (e.g. URI, URL, text, xsd:boolean):** ``` xsd:string ``` **Description**...

matentzn

Add tutorial on how to pick the right mapping predicate

2

It is frequently confusing to people to see mapping predicates like - skos:closeMatch and oboInOwl:hasDbXref - skos:exactMatch and owl:equivalentClass side by side. Beyond the [spec](https://mapping-commons.github.io/sssom/spec/#common-mapping-predicates) we should provide a better...

matentzn

Side-by-side BioPortal/OntoPortal format - SSSOM comparison

4

This is similar to #147 We have started such a process in AgroPortal : https://github.com/agroportal/project-management/issues/265 CC @graybeal

jonquet

Side-by-side comparison FHIR ConceptMap and SSSOM

11

https://www.hl7.org/fhir/conceptmap.html and SSSOM are obviously very different in scope, but it would be useful to explore commonalities and places for alignment. @DaveraGabriel is working with @joeflack4 on a cursory alignment...

matentzn

is there interest in an analog of SSSOM for NER/CR/text annotation?

15

There are a number of different tools that perform NER on text, from bioportal/zooma through to scispacy, @cthoyt's Gilda ( gilda https://www.biorxiv.org/content/10.1101/2021.09.10.459803v1.full ) These all vary in their output but...

cmungall

Declare identifiers in linkml model

1

We should make sure that identifers like `mapping_set_id` or `mapping_registry_id` are declared as LinkML identifiers. _Originally posted by @matentzn in https://github.com/mapping-commons/sssom/pull/159#discussion_r852281360_

matentzn

Representing data model elements and their values in SSSOM

32

Case: we want to map literal values in a set of permissible values in a data model (say "M" in gcs.maritalstatus) to some ontology term `NCIT:Married`. Now there might not...

matentzn

Lexical match metadata

3

Currently we include preprocessing and match fields for lexical matches, but there are other things to consider like: - edit distance (threshold based, like semantic similarity, some kind of `lexical_similarity_score`....

matentzn

Make recommendation to split negated mappings in separate files

3

We have often warned of the dangers of allowing negative (NOt) and positive mappings side by side due to the possibility of accidentally ignoring the predicate_modifier column by more naive...

matentzn