Skip to content

DOSDP pattern creation and edits

Jump to bottom
Nico Matentzoglu edited this page Aug 23, 2023 · 11 revisions

General DOSDP notes

These are notes for how to create DOSDP patterns from scratch, but these notes also have information about how to add new terms to previously made patterns. The information is specific to the MAXO repo, but could be applied to other repos.

Creation of the DOSDP pattern/YAML file

Open a text editor and call the file 'name_of_pattern.yaml' and save file in this folder: https://github.com/monarch-initiative/MAxO/tree/master/src/patterns/dosdp-patterns

Anatomy of a yaml file

Introduction

  • pattern name
  • pattern iri
  • description
  • contributors
  • Pattern name: This is a simple name that gives a reasonable description of what the pattern is for. Note: Using 'location' in MAxO's context is the 'location on the body' and thus UBERON ontology is used for building terms and logical statements.

pattern_name: specimen_collection_by_location.

  • Pattern IRI: This is where the file can be found.

pattern_iri: http://purl.obolibrary.org/obo/maxo/patterns/specimen_collection_by_location.yaml

  • Pattern description: A brief synopsis about what the pattern is trying to do.

description: "Collection of biological material, particularly fluids for clinical use".

  • Pattern contributors: List of contributors orcid IDs for reference and for being able to identify who to speak with about a problem. If you update or add to a pattern, please add your orcid ID.

contributors:

  • Classes: List of classes used in logical definitions. This is usually where you want to insert the terms in MAxO and the top of the branch in the other ontology

classes:

collection: MAXO:0000547

location: owl:Thing

  • Relations: these are the ontology terms for relations ontology (RO) used in creating the logical definitions

relations:

has_input: RO:0002233

part_of: BFO:0000050

  • Annotation properties: These are all the properties that are potentially used to build annotations

annotationProperties:

exact_synonym: oio:hasExactSynonym

created_by: oio:created_by

date: dc:date

comment: rdfs:comment

xref: oio:hasDbXref

  • Vars: This is the variable field from the external ontology. These variables are coming from a parallel TSV file with the same name. More information below.

    vars:

    > location: "'location'"

  • Data Vars: These are the annotation fields that are not based on anotations. These variables are coming from a parallel TSV file with the same name. More information below. Note, these fields only can add a single annotation.

data_vars:

date: "'date'"

created_by: "'created_by'"

comment: "'comment'"

xref: "database cross reference"

  • Data list vars: These are annotations that have more than one annotation in the TSV file. In the TSV file, the terms are separated by " | "

data_list_vars:

> syns: xsd:string
  • Name/definition/Annotation fields: There are several different types that all have roughly the same sort of anatomy

  • Equivalent to: This is where you create a logical definition based on your term.

TSV FILE

TSV files for patterns need to be in this folder: https://github.com/monarch-initiative/MAxO/tree/master/src/patterns/data/manual

These are simple to set up just following basic schema. Note, the name of the file must exactly match the yaml file, but with TSV suffix.

Note: Defined class and location are the only 2 fields required for the term to be built. -defined class: A new or current MAXO id can be used, but if you use a currently created maxo term, all labels will be doubled. Please see below for where to find MAXO ID

  • defined class name: This isn't required. If you don't fill anything in, the pattern will generate a label. If you do include something in the this field, it will override the pattern
  • location: required field from ontology you want to build a term from
  • location label: not required, but it makes it easier to determine what term you are building
  • created by: not absolutely required, but it is good to include orcid ID
  • date: Use the current date in this format. Don't worry about the time
  • defined class definition: this field overrides the pattern definition.
  • comment: use this field if you need to add a comment
  • xref: Use this for xref for the entire term. Note, there is no way (currently) to add a xref only for a comment or definition using patterns.
  • syns or synonyms: This is available for adding additional synonyms not built by the pattern. This is the only field where you can include multiple terms, but they must be separated bye " | "

MAXO IDS for patterns

When not using protege, you have to add your own MAXO IDS. To do this, use the file stored here: https://github.com/monarch-initiative/MAxO/blob/master/src/patterns/data/todo/MAXO_availableIDs.txt

This is a text file with available IDS. just copy/paste into the TSV files making absolutely sure you delete the IDs in this TSV file that you have used for the DOSDP pattern TSV.

UPDATE DEFINITIONS.OWL

  • Previously ran release to update patterns to see terms. However, only need to run definitions update. sh run.sh make ../patterns/definitions.owl IMP=false MIR=false
Clone this wiki locally