Systems and methods for automatically identifying and linking names in digital resources

1. A method for identifying relationships between information objects and first digital resources, the method comprising:

building a graph of information objects retrieved from a database, wherein

each information object comprises structured text, data, and metadata representing an entity in digital form, said entity being one of: name, taxon, exemplar, practitioner, or nomos,

each information object is identified by at least one persistent globally unique identifier, wherein said persistent globally unique identifier resolves to a service or a second digital resource encoding said structured text, data, and metadata for said information object,

said graph comprises a set of information objects and relations among said information objects, each relation linking a pair of information objects,

each said pair comprising entities of type: name-name, name-taxon, taxon-taxon, taxon-exemplar, exemplar-exemplar, nomos-taxon, practitioner-name, practitioner-taxon, practitioner-exemplar, or practitioner-nomos, and

each said pair including a relation representing one of: synonymy, homonymy, orthographic variation, equivalence, membership, supertype, or subtype,

new relations among said information objects are inferred based on a set of encoded rules, and

the information objects in said graph may be traversed over said relations;

searching within parsed data of a first digital resource for occurrences of name-like-strings, comprising at least one of the following steps

searching within the parsed data for specialized formatting,

searching within the parsed data for a string satisfying a regular expression,

analyzing the parsed data using a grammar constructed for a class of name, performing a text search within the parsed data against a reference list of names, or

performing a text search within the parsed data to identify a string having at least one of a known prefix or suffix used in a terminology,

for each name-like-string identified in the parsed data:

creating metadata marking an exact location in the parsed data of the occurrence of said name-like-string,

obtaining a first persistent globally unique identifier of an information object by matching said name-like-string against the names or labels of entities, wherein said entities are represented as information objects stored in a repository, and wherein each information object is identified by a unique identifier,

retrieving a first information object from said graph, wherein said first persistent globally unique identifier is identical to a second persistent globally unique identifier that identifies said first information object;

analyzing said graph, wherein the analysis

traverses said graph from said first information object over said relations to identify a plurality of information objects related to said first information object, and

retrieves a second information object from among the information objects comprising said graph;

obtaining from said second information object a third persistent globally unique identifier,

creating a new relationship associating said second information object with the first digital resource, wherein said relationship comprises said third persistent globally unique identifier for said information object, a content identifier for said digital resource, and metadata about said association, and

storing said relationship in a database,

wherein each information object identifier is one of a Digital Object Identifier (DOI), a Handle, an Archival Resource Key (ARK), a Persistent Uniform Resource Locator (PURL), a Universal Unique Identifier (UUID), a Globally Unique Identifier (GUID), or a Life Sciences Identifier (LSID), and

wherein said digital resource may be uniquely identified by at least one content identifier comprising a Digital Object Identifier (DOI), a Handle, an Archival Resource Key (ARK), a Persistent Uniform Resource Locator (PURL), a Universal Unique Identifier (UUID), a Globally Unique Identifier (GUID), or a Uniform Resource Identifier (URI),

wherein said metadata about the association comprises at least one of said name-like-string, said exact location of said name-like-string in said parsed data, a number of occurrences of said second information object in the first digital resource, and a number of times said second information object is accessed from its relationship with the first digital resource.

2. The method of claim 1 , wherein said content identifier for an information object may additionally be any Uniform Resource Identifier (URI) that both globally and uniquely identifies said information object.

3. The method of claim 1 , wherein said digital resource includes a computer-storable item selected from the group consisting of: scientific, technical, and medical (STM) literature, patents, Biological Resource Center (BRC) databases, legal literature, diagnostic machinery databases, contracts, treaties, material transfer agreements, prior informed consent, certificates of origin, other documents establishing provenance, bills of lading, shipping documents, specification sheets, interactive graphics, and regulations or laws as applied to holding, transportation, or working with an organism.

4. A system configured to carry out the method of claim 1 , wherein the system comprises a plurality of computers, each with software, with the computers communicating via an electronic medium and each performing part of the overall process, and wherein the digital resource is non-transitory.

5. The method of claim 1 , wherein said digital resource is a web page.

6. A system configured to carry out the method of claim 5 , wherein the system comprises an add-on, extension, or plug-in for a web browser that operates on the parsed data of the digital resource.

7. A system configured to carry out the method of claim 6 , wherein matching said name-like-string against the names or labels of entities, wherein said entities are represented as information objects stored in a repository is performed by a web service.

8. A system configured to carry out the method of claim 1 , wherein the system comprises an add-on, extension, or plug-in for a document editor that operates on the parsed data of the digital resource.

9. A system configured to carry out the method of claim 1 , wherein said relation additionally comprises said exact location of said occurrence of said name-like-string in said first digital resource.