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

1. A method for adding tags to a first digital resource, 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 a first structure 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 graphs;

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

adding said third persistent globally unique identifier to said first structured metadata,

modifying said first digital resource by inserting said first structured metadata at said exact location in the parsed data of the first digital resource.

2. The method of claim 1 , wherein said identifier is at least one of a Digital Object Identifier (DOI), a Handle, a Uniform Resource Identifier (URI) or a Uniform Resource Name (URN), an Archival Resource Key (ARK), a Persistent Uniform Resource Locator (PURL), a Universal Unique Identifier (UUID), a Globally Unique Identifier (GUID), and a Life Sciences Identifier (LSID).

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 agreements, 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.

5. The method of claim 1 , wherein said first digital resource is a web page and said first structured metadata conforms to an HTML specification.

6. The method of claim 5 , wherein said first structured metadata is associated with an actionable service, and

said first structured metadata is an active region that responds to End-User behavior,

said actionable service is invoked as a result of End-User activity and

said actionable service uses said third persistent globally unique identifier to retrieve additional content from a remote server and

said additional content is presented to said End-User.

7. The method of claim 6 , wherein said additional content comprises additional actionable services.

8. The method of claim 1 , wherein said first digital resource is a Document Object Model and said first structured metadata comprises a set of Document Object Model nodes.

9. The method of claim 1 , wherein said first digital resource is an XML document and said first structured metadata comprises well-formed XML.

10. The method of claim 1 , wherein said first digital resource conforms to Open Office XML format and said first structured metadata conforms to Open Office XML format.

11. The method of claim 1 , wherein said first structured metadata comprises additional data from one or more information objects.