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prefix_tool_functions.txt
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Summary of Scenarios
(derived from material in https://docs.google.com/document/d/1DxU2IN56fUoASxaiEOsn2NDtjRGWw5rK_BxRAKcyvwU/edit)
*** Database providers (incl. material resource providers)
1) The preferred prefix for our database is FOOBAR; is this prefix available or taken?
1a) If it appears to be registered:
1b) If the prefix FOOBAR hasn’t been “taken” (registered anywhere):
*** Researchers
2) What is known about Optic disk coloboma (HP:0000588)?
3) HP:0000588. What is the authoritative original source of this information and what is the URL whereby can I access it?
4) what might this refer to?
5) What is known about this entity?
6) how can I determine the impact of this resource?
*** Data aggregators (including publishers)
7) I want to reference identifiers for the Human Phenotype Ontology in our database. Should I use the prefix HP or HPO?
8) In our application we aggregate / integrate data from dozens of sources. I would like to document:
9) I would like to know which other data sources or tools might have data relevant to sources we XREF;
10) Our database needs to reference the Gene Expression Omnibus and the GeoNames Ontology, but both of these lay claim to the “GEO” prefix.
11) What are all of the known preferred prefix collisions in the prefixome.
12) I see records that a given prefix is assigned to two databases by slightly different names and URLs. Are these in fact the same database?
13) REST API to convert URLS them back into the provider-issued CURIE prefix
14) I want to reference HP identifiers, what are all of the different locations of this exact record?
*** Funders
(Not filled in for now; but included in the function list below)
The following list of categorized functions came from the original document (summarized above), and materials developed during the hackathon.
Categorizing Prefix Functionality
*** Understanding Prefixes
prefix available or taken
most credible target for prefix
in which registry/ies
Documentation: For given registry's entry for this prefix:
- Primary prefix
- Alternate prefix
- Entity identifier (e.g., IRI)
- Identifier namespace path if different (e.g., includes # or / separator)
- identifier resolution - computable (y/n)
- identifier resolution - human viewable (y/n)
- different namespace for human readable pages
- homepage
- description
- title
- more detailed metadata about the entry
- Local identifier (e.g., DB record key)
- who registered
- when registered
*** Understanding Prefixes: Errors
prefix clashes - one prefix, multiple resources
prefix ambiguity - one prefix, maybe multiple resources
redundant primary prefixes per resource - more than one prefix
*** Registering Prefixes
where to register
how to streamline registration
how to cite
how to register data source
how to specify format of data source
how to specify metadata re data source
how to correct metadata re data source
where to manage metadata re data source
minimum metadata required (new)
*** Prefix Application/Citation
prefix user count
prefix user list
prefix subscriber list
prefix user general contact method
prefix user 'request link' contact method
prefix user registry synchronization
prefix impact profile
prefix impact profile over time
prefix impact profile relative to average
prefix record locations
*** Prefixed Entity Lookup
entity information
entity resolvable URL
how to resolve entity of form X
how to get computable representation of entity(ies)
entity authoritative source
entity annotations locations
entity tools
entity purchase information
entity users
entity meta-information subscription
entity impact
*** Using Prefixes
which prefix to use (differentiation, disambiguation)
alternate prefix to use (conflict avoidance)
which prefixes we use
which external sources we use
*** Prefix Environment
known preferred prefix collisions
known prefix collisions (including alternates)
prefix issue resolution (clashes, ambiguity, redundancy, metadata errors)
*** Prefix Discovery
from URL
from context (roughly, faceted search)
quantified by research space (gaps and overlaps)