LinkML Registry Entries

LinkML Schema Metamodel

A metamodel for defining linked open data schemas

key value
name LinkML Model
title LinkML Schema Metamodel
homepage https://linkml.github.io/linkml-model/docs/
schema_url https://github.com/linkml/linkml-model/blob/main/model/schema/meta.yaml
github_repo linkml/linkml-model
schema_relative_path model/schema/meta.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics meta
class_count 19
slot_count 125
enum_count 1
type_count 14
github_stars 10
proportion_elements_with_a_description 0.91
proportion_elements_mapped 0.99

LinkML template configuration

None

key value
name LinkML Template Configuration Model
title LinkML template configuration
homepage https://linkml.github.io/template-config-model/
schema_url https://github.com/linkml/template-config-model/blob/main/model/schema/config_model.yaml
github_repo linkml/template-config-model
license CC-0
topics meta
github_stars 1

NMDC Schema

Schema for National Microbiome Data Collaborative (NMDC). This schem is organized into 3 separate modules:

This schema is organized into distinct modules:

  • a set of core types for representing data values
  • the mixs schema (auto-translated from mixs excel)
  • annotation schema
  • the NMDC schema itself
key value
name NMDC
title NMDC Schema
homepage https://microbiomedata.github.io/nmdc-schema/
github_repo microbiomedata/nmdc-schema
schema_relative_path src/schema/nmdc.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics environmental microbiology
class_count 48
slot_count 884
enum_count 1
type_count 18
github_stars 5
proportion_elements_with_a_description 0.86
proportion_elements_mapped 0.99

Entity and association taxonomy and datamodel for life-sciences data

key value
name Biolink-Model
title Biolink Model
homepage https://biolink.github.io/biolink-model/
github_repo biolink/biolink-model
schema_relative_path biolink-model.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics genomics; disease; phenotype; expression; GO; GO-CAM; human biology; model organism biology; biochemistry; biology
class_count 257
slot_count 608
enum_count 9
type_count 27
github_stars 68
proportion_elements_with_a_description 0.67
proportion_elements_mapped 0.99

Simple Standard Sharing Object Mappings

Datamodel for Simple Standard for Sharing Ontology Mappings (SSSOM)

key value
name SSSOM
title Simple Standard Sharing Object Mappings
homepage https://sssom-py.readthedocs.io/
github_repo mapping-commons/sssom-py
schema_relative_path schema/sssom.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics information
class_count 3
slot_count 49
enum_count 1
type_count 14
github_stars 10
proportion_elements_with_a_description 0.98
proportion_elements_mapped 0.98

Knowledge Graph Change Language

None

key value
name KGCL
title Knowledge Graph Change Language
homepage https://cmungall.github.io/knowledge-graph-change-language/
github_repo cmungall/knowledge-graph-change-language
schema_relative_path src/schema/kgcl.yaml
license CC-0
topics knowledge graphs
github_stars 13
errors Error with obtaining schema for KGCL: Conflicting URIs (https://w3id.org/kgcl/basics, https://w3id.org/kgcl/prov) for item: description

Knowledge Graph Visualization Configuration

A data model for describing configurations / stylesheets for visualzing graphs, and in particular Knowledge Graphs or Ontologies. These graphs are characterized by having meaningful edge labels, node categories, IDs or URIs on each element, as well as additional rich metadata on the nodes or edges. An example of a use of this is https://github.com/cmungall/obographviz

key value
name KGViz
title Knowledge Graph Visualization Configuration
homepage https://berkeleybop.github.io/kgviz-model/
github_repo berkeleybop/kgviz-model
schema_relative_path model/schema/kgviz.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics visualization
class_count 16
slot_count 30
enum_count 3
type_count 16
github_stars 4
proportion_elements_with_a_description 0.53
proportion_elements_mapped 0.95

Semantic SQL

A datamodel for RDF, OWL, and OBO Ontologies designed to work harmoniously with SQL databases.

Note that the primary purpose of this linkml schema is to organize and define SQL VIEWs to be used on top of a generic SQL database following the rdftab statements schema. These SQL views are encoded with the sqlviews>> tag inside the yaml.

We use linkml to do this rather than a simple SQL DDL file because linkml gives us a standard way to do things such as:

  • attach descriptions to each view
  • define a data dictionary of all columns used, together with domains/ranges
  • modular structure with imports
  • the ability to attach rich semantic metadata to each schema element

Additionally, the framework provides automatic compilation to SQLAlchemy models, and tools for being able to turn views into indexed tables for efficient querying, as well as a rich searchable documentation system and other tooling.

This schema is best browsed online: https://cmungall.github.io/semantic-sql/

Note that things are in flux, and there some oddities that need ironed out, see issues for details

See the github repo for code to convert from the linkml yaml into SQL DDL

key value
name Semantic Sql
title Semantic SQL
homepage https://cmungall.github.io/semantic-sql/
github_repo cmungall/semantic-sql
schema_relative_path src/schema/semsql.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics ontologies
class_count 98
slot_count 80
enum_count 0
type_count 16
github_stars 10
proportion_elements_with_a_description 0.58
proportion_elements_mapped 1.0

Chemistry Data Model

A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures. Aspects of this have been cribbed from various sources including CHEBI, SIO, Wikipedia/Wikidata, the NCATS Translator Chemical Working Group, but all mistakes are my own. For full context/motivation see the GitHub repo.

key value
name Chemistry Schema
title Chemistry Data Model
homepage https://cmungall.github.io/chem-schema/
github_repo cmungall/chem-schema
schema_relative_path src/schema/chem.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics chemistry
class_count 120
slot_count 266
enum_count 5
type_count 22
github_stars 7
proportion_elements_with_a_description 0.46
proportion_elements_mapped 0.99

CRDC-H Model

None

key value
name CCDH
title CRDC-H Model
homepage https://cancerdhc.github.io/ccdhmodel
github_repo cancerdhc/ccdhmodel
schema_relative_path src/schema/ccdhmodel.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics cancer
class_count 41
slot_count 333
enum_count 108
type_count 21
github_stars 10
proportion_elements_with_a_description 0.99
proportion_elements_mapped 0.78

common association file formats

Various association data models

key value
name ontology-associations
title common association file formats
homepage https://biodatamodels.github.io/ontology-associations/
github_repo biodatamodels/ontology-associations
schema_relative_path src/schema/all.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics genomics
class_count 33
slot_count 124
enum_count 18
type_count 25
github_stars 4
proportion_elements_with_a_description 0.31
proportion_elements_mapped 0.94

Genome Feature Format LinkML rendering

Playing around with GFF spec

key value
name GFF3
title Genome Feature Format LinkML rendering
homepage https://biodatamodels.github.io/gff-schema/
github_repo biodatamodels/gff-schema
schema_relative_path src/schema/gff.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics genomics
class_count 8
slot_count 38
enum_count 3
type_count 16
github_stars 5
proportion_elements_with_a_description 0.56
proportion_elements_mapped 0.95

Chromosome ontology and ETL

None

key value
name Monochrom
title Chromosome ontology and ETL
homepage https://monarch-initiative.github.io/monochrom/
schema_url https://github.com/monarch-initiative/monochrom/blob/master/model/schema/chromo.yaml
github_repo monarch-initiative/monochrom
license CC-0
topics genomics
github_stars 8

None

key value
name GSC MIxS
topics genomics

A schema for describing translations and language profiles for ontologies

None

key value
name Babelon
title A schema for describing translations and language profiles for ontologies
homepage https://matentzn.github.io/babelon/
github_repo matentzn/babelon
license CC-0
topics ontologies
github_stars 1

HOT-TermCI

Terminology Core Common Model

key value
name HOT-TermCI
title HOT-TermCI
homepage https://github.com/HOT-Ecosystem/TermCI-model
github_repo HOT-Ecosystem/TermCI-model
schema_relative_path src/schema/tccm_schema.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics clinical
class_count 4
slot_count 16
enum_count 0
type_count 14
github_stars 3
proportion_elements_with_a_description 0.97
proportion_elements_mapped 1.0

Alliance of Genome Resources Persistent Schema

Alliance Persistent Schema

key value
name Alliance of Genome Resource Persistent Schema
title Alliance of Genome Resources Persistent Schema
github_repo alliance-genome/agr_curation_schema
schema_relative_path src/schema/alliance_schema.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
topics genomics
github_stars 3
errors Error with obtaining schema for Alliance of Genome Resource Persistent Schema: [Errno 2] No such file or directory: '/Users/cjm/repos/linkml-registry/tmp/agr_curation_schema/src/schema/alliance_schema.yaml'

None

key value
name SESAR
topics earth science

None

key value
name OBOGraphs
github_repo biodatamodels/obograph
topics ontologies
github_stars 3

Metadata schema for the German Human Genome-Phenome Archive (GHGA)

None

key value
name GHGC Metadata
title Metadata schema for the German Human Genome-Phenome Archive (GHGA)
homepage https://ghga-de.github.io/ghga-metadata-schema/
github_repo ghga-de/ghga-metadata-schema
schema_relative_path src/schema/ghgc.yaml
github_stars 3
errors Error with obtaining schema for GHGC Metadata: [Errno 2] No such file or directory: '/Users/cjm/repos/linkml-registry/tmp/ghga-metadata-schema/src/schema/ghgc.yaml'

Minimal Information About a new Cell Type

This schema is CJM's attempt to translate Tiago's minimal info doc into a LinkML schema

The schema is fairly minimal and is in the form of a "checklist" style schema. It is a set of fields mostly associated with this class:

There are a set of examples here:

Currently the examples are YAML, but the YAML is deliberately flat as this is a "checklist" schema, and we could have TSV/CSV/xlsx here

TODO:

  • include "packages" and "checklists"; e.g.
    • a neuron package would have the enum for morphologies constrained
    • a transcriptomics package would make it required to enter the set of marker genes
    • see MIxS schema for example of how this might work
  • document how this relates to dosdp/robot templates

When should one provide an entry for a cell type in a MIANCT sheet?

  • When there is a claim of a new cell class (type or state) that has not been described before
  • When new information is discovered for a previously cataloged type that might influence its cataloguing (i.e. description of the presence in a different species or in a new location)
  • When a cell type mentioned in the article has been described before, but is not yet catalogued on an authoritative source like the Cell Ontology.
key value
name MIANCT
title Minimal Information About a new Cell Type
homepage https://cmungall.github.io/mianct-schema/
github_repo cmungall/mianct-schema
schema_relative_path model/schema/mianct.yaml
license https://creativecommons.org/publicdomain/zero/1.0/
class_count 2
slot_count 11
enum_count 3
type_count 15
github_stars 3
proportion_elements_with_a_description 0.64
proportion_elements_mapped 0.93