New term request how to

Marcus Chibucos edited this page Apr 1, 2016 · 4 revisions

Template for requesting a new term

Purpose of this document

This document contains general guidelines used by ECO developers for standardizing term development. Biocurators, ontologists, database managers, and anyone else wishing to create new ECO terms are encouraged to consider the points below. Although you are not required to follow our template for new term requests, doing so will increase the likelihood and speed of your term being added to ECO.

Points to consider regarding new term requests

  1. Succinct term name (label) in the form of evidence, for example "microscopy evidence" or "motif discovery evidence". Many ECO experimental evidence types can be thought of as recorded information derived from a process (e.g. performing an assay) that has inputs of various components (e.g. machines, instruments, reagents, samples) and has outputs of various data types (e.g. images, tables, figures).

  2. Aristotelian definition, in the form of "B is an A that C's". In other words, consider exactly what characteristics (C) make this term (B) a more specific subtype of the parent term (A). Consider also what distinguishes this term from other proposed or existing terms sharing its parent. For example, the term "traceable author statement" is a subclass (child term) of "author statement". The definition of "traceable author statement" is "An author statement that is based on a cited reference". A related term with the same parent, "non-traceable author statement", is defined as "An author statement that is not associated with results presented or a cited reference." As subclasses of the same parent, these terms share common attributes, i.e. they are both author statements, but they each have distinguishing characteristics that are specific and non-overlapping, as well.

    Definitions should be succinct and fit into one sentence, but they should contain as much information as is required to capture the meaning of the term. Additional comments, examples, or usage notes should be provided in a separate comments section and not merged into the definition. This will prevent unnecessarily restricting the meaning of terms so that they can only be used by a specific database (usually the term creator's database).

    [Please help us refine ECO: if you encounter a problem with a particular existing term label, definition, or position within the ontology, create an issue on our GitHub site. It's never a bad idea to search issues first to see if there is an existing one or a related one that you can add to or refer to.]

  3. Suggest a parent term, either existing or new. As you are researching your term's definition, make a note of its most appropriate parent term. In general, ECO is trying to follow a single inheritance hierarchy, where each term has one parent. If you feel that more parents are appropriate or necessary, then note this and we can create appropriate logical definitions to allow for inferring these relationships.

  4. Provide a reference for the definition, preferably in the form of a PubMed ID. Preferred references are papers that are free (i.e. no paywall) and easy to access for most people.

  5. Additional information can be shared. Writing clear, detailed, succinct definitions requires full knowledge of a subject. There are many types of additional information that can help us write better definitions & comments and clarify subtleties in meaning. These include:

  • additional references or hyperlinks to articles
  • personal notes on ECO term use in curation
  • examples of ECO terms in use by other resources
  • personal notes about the techniques (experimental or computational) described by a requested term
  • knowledge about terms similar to ECO terms at other ontologies, databases, and other resources
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