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make the infores catalog itself downloadable and viewable from homepa…
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| Original file line number | Diff line number | Diff line change |
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| ## InfoRes Catalog Metadata Dictionary | ||
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| At present, a minimal set of metadata is being collected in the InfoRes Registry using the following Biolink node | ||
| properties, which will be expanded in future iterations. | ||
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| name: a fully informative name for the resource (we recommend a name that is as informative and unambiguous as | ||
| possible - spelling out all acronyms that are not common knowledge, and including the name of the owning organization | ||
| when the name alone may be ambiguous). | ||
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| id: the CURIE form of the InfoRes identifier, wherein a short form name of the resources serves as a human readable | ||
| identifier component (e.g. ‘infores:dgidb’) | ||
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| * **synonym**: | ||
| * other names for the resource (will facilitate search/discovery) | ||
| * **url**: | ||
| * a url describing the resource - preferably its primary home page for the resource (if one exists) | ||
| * **description**: | ||
| * a free text description of the resource | ||
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| ## Rules for Minting InfoRes Names and Identifiers | ||
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| A short form human understandable name or abbreviation is used as the identifier component of an InfoRes IRI, | ||
| and should follow these conventions: | ||
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| * Use lowercase characters only. | ||
| * Keep as short as possible while remaining understandable and unambiguous. | ||
| * Acronyms are good where they are well-established and used in practice in our domain (e.g. infores:omim, not infores:online-mendelian-inheritance-in-man). Otherwise, spell out the name to the extent needed to be understood by the user (e.g. infores:drug-repurposing-hub, not infores:drh). | ||
| * Where it makes sense to do so, adopt the base url of the resources home web address, or its registered prefix in an authority like identifiers.org. | ||
| * Use a hyphen (-) to separate words where needed (e.g. infores:drug-repurposing-hub), unless the words are not separated in common practice or the website url (e.g. we use infores:monarchinitiative, not infores:monarch-initiative, because their website is https://monarchinitiative.org/). | ||
| * All other non-alphanumeric characters are not allowed as delimiters. | ||
| * If we begin creating version-specific identifiers, a dot (.) will be reserved as a separator between the base resource name and its version. And versions will be specified using either dot-separated numerals (e.g. '1.1.2'), or release dates in ISO8601 format (e.g. '2021-04-18'). | ||
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| ## Conventions for Crafting Identifiers for Translator Registry Resources | ||
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| Translator applies many services that wrap or annotate existing resources in APIs to serve content that is better | ||
| aligned with Translator standards. This practice can lead to confusion around what represents a separate Information | ||
| Resource, and how resources may be related to each other. Below we describe conventions we apply for InfoRes creation | ||
| for different scenarios / use cases we encounter in the registry. | ||
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| Aggregator Scenario: KPs/ARAs that aggregate content from one or more existing resource and transform the semantics | ||
| and or structure of the data to be better aligned with Translator standards | ||
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| Resource Examples: | ||
| Molecular Data Provider, Biolink, ROBOKOP, SRI Reference KG, RTX KG2 (these aggregate content from multiple sources into a single KG / API) | ||
| Automat APIs (stands up a separate API per source - each of which gets its own InfoRes) |
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| ## Biolink Edge Properties for Source Retrieval Provenance | ||
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| We define the following hierarchy of edge properties in Biolink for capturing Information Resources through which | ||
| knowledge expressed in a given edge was retrieved on its way to its presently serialized form (e.g. a TRAPI message | ||
| sent to an ARA). Full definitions and metadata for each can be found in the Biolink Model. | ||
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| * **biolink:knowledge_source**: | ||
| * An Information Resource from which the knowledge expressed in an Association was retrieved, | ||
| directly or indirectly | ||
| * **biolink:primary_knowledge_source**: | ||
| * The most upstream source of the knowledge expressed in an Association that a | ||
| knowledge provider can identify. | ||
| * **biolink:aggregator_knowledge_source**: | ||
| * An intermediate aggregator resource from which knowledge expressed in an | ||
| Association was retrieved downstream of the original source, on its path to its current serialized form. | ||
| * **`biolink:supporting_data_source`**: | ||
| * An Information Resource from which data was retrieved and subsequently used as | ||
| evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference | ||
| over the retrieved data). | ||
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| ## The Information Resource Registry (infores) data model | ||
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| An information resource is defined as a web-accessible resource that provides data. An InformationResource | ||
| (designated by its identifier in curie form, e.g. 'infores:monarchintiative') is a Biolink Model class that provides | ||
| a standard way to identify and describe information resources. The InformationResource class details can be found here: | ||
| [information_resource_registry.yaml](information_resource_registry.yaml) and contains the following properties: | ||
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| - **id**: the identifier of the information resource (e.g. 'infores:monarchintiative') | ||
| - **name**: the name of the information resource (e.g. 'Monarch Initiative') | ||
| - **description**: a description of the information resource (e.g. 'Monarch is a platform for biomedical data discovery | ||
| and integration') | ||
| - **url**: the url of the information resource (e.g. 'https://monarchinitiative.org/') | ||
| - **status**: the status of the information resource (e.g. 'released', 'deprecated', etc. Please see the enumeration | ||
| listed in the model yaml for more information) |
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