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Record W2023917861 · doi:10.1038/npre.2010.5060.1

Bio2RDF: Convert, Provide And Reuse.

2010· preprint· en· W2023917861 on OpenAlex

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

VenueNature Precedings · 2010
Typepreprint
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicBiomedical Text Mining and Ontologies
Canadian institutionsCarleton UniversityUniversité Laval
Fundersnot available
KeywordsComputer scienceIdentifierSPARQLLinked dataRDFInformation retrievalWorld Wide WebSemantic WebDatabaseData science

Abstract

fetched live from OpenAlex

Abstract The Bio2RDF project uses open-source Semantic Web technologies to provide interlinked life science data in order to maximize productivity and facilitate biological knowledge discovery. Using both syntactic and semantic data integration techniques, Bio2RDF puts into practice a simple methodology to generate and seamlessly integrate machine-interpretable data that can be powerfully interrogated with SPARQL-based queries to answer sophisticated questions.At its core, database records are converted into a set of statements or so-called triples that are captured together as a named graph annotated with provenance. The records and the entities they are about are provided with a Uniform Resource Identifier (URI) of the form http://bio2rdf.org/prefix:identifier, where the prefix indicates a reserved name for the dataset, record or terminological resource. The application of this simple method allows resources from over 40 datasets to integrate seamlessly at the syntactic level irrespective of whether the original data contains non-Bio2RDF URIs.However, when original data providers such as Uniprot provide their own RDF they will rightfully use URIs that resolve to their servers, but what should they do for externally defined entities? If they follow in Bio2RDF’s footsteps then every data provider will use a different URI. However, should original data providers present and implement a URI scheme, then it becomes possible for others to establish stable links to their resources. As such, we will witness the birth of a more stable linked data network, ensuring that data providers need not provide third party data in a redundant manner.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.002
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow), Research integrity
Consensus categoriesResearch integrity
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.668
Threshold uncertainty score1.000

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.002
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0010.002
Research integrity0.0040.003
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.008
GPT teacher head0.277
Teacher spread0.269 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it