Package: ducksemantics 0.1.0

Sounkou Mahamane Toure

ducksemantics: DuckDB-Native Semantic Graph Grounding

DuckDB-native semantic graph grounding over arbitrary concept graphs. The package owns graph schema creation, alias indexing, lexical mention grounding, transitive graph closure, 'EmbeddingGemma' dense retrieval, 'ColBERT' late interaction, and 'BebeLM' judgment prompts. HPO, MONDO, ORPHANET, memory graphs, and run ledgers are graph sources, not special package APIs.

Authors:Sounkou Mahamane Toure [aut, cre], Human Phenotype Ontology [cph]

ducksemantics_0.1.0.tar.gz
ducksemantics_0.1.0.zip(r-4.7)ducksemantics_0.1.0.zip(r-4.6)ducksemantics_0.1.0.zip(r-4.5)
ducksemantics_0.1.0.tgz(r-4.6-any)ducksemantics_0.1.0.tgz(r-4.5-any)
ducksemantics_0.1.0.tar.gz(r-4.7-any)ducksemantics_0.1.0.tar.gz(r-4.6-any)
ducksemantics_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ducksemantics/json (API)

# Install 'ducksemantics' in R:
install.packages('ducksemantics', repos = c('https://rgenomicsetl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sounkou-bioinfo/ducksemantics/issues

On CRAN:

Conda:

2.18 score 1 stars 71 exports 3 dependencies

Last updated from:a21153a947. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK168
source / vignettesOK237
linux-release-x86_64OK167
macos-release-arm64OK162
macos-oldrel-arm64OK176
windows-develOK225
windows-releaseOK222
windows-oldrelOK224
wasm-releaseOK157

Exports:ducksemantics_annotateducksemantics_bebel_judgeducksemantics_bebel_runnerducksemantics_bebel_tool_judgment_parserducksemantics_benchmarkducksemantics_benchmark_casesducksemantics_benchmark_metricsducksemantics_cache_fileducksemantics_cache_rdsducksemantics_closure_sqlducksemantics_cluster_embeddingsducksemantics_colbert_providerducksemantics_colbert_queryducksemantics_connectducksemantics_default_judgment_instructionsducksemantics_embedducksemantics_embed_cachedducksemantics_embedding_batchducksemantics_embedding_cluster_graph_agreementducksemantics_embedding_cluster_specducksemantics_embedding_cluster_summaryducksemantics_embedding_index_specducksemantics_embedding_providerducksemantics_embedding_queryducksemantics_embedding_searchducksemantics_embeddinggemma_providerducksemantics_groundducksemantics_index_aliasesducksemantics_index_statsducksemantics_initducksemantics_json_judgment_parserducksemantics_judgeducksemantics_judgment_promptducksemantics_late_interaction_searchducksemantics_lexical_annotatorducksemantics_materialize_embedding_indexducksemantics_normalizeducksemantics_parseducksemantics_projection_sqlducksemantics_prompt_runnerducksemantics_read_oboducksemantics_record_judgmentsducksemantics_runducksemantics_schema_sqlducksemantics_tablesducksemantics_token_embedducksemantics_token_embedding_batchducksemantics_token_embedding_batch_from_providerducksemantics_token_embedding_providerducksemantics_token_embedding_queryducksemantics_tokensducksemantics_write_embeddingsducksemantics_write_graphducksemantics_write_oboducksemantics_write_token_embeddingsDucksemanticsAnnotatorDucksemanticsDbConnectionDucksemanticsEmbeddingBatchDucksemanticsEmbeddingClusterSpecDucksemanticsEmbeddingIndexSpecDucksemanticsEmbeddingMatrixDucksemanticsEmbeddingProviderDucksemanticsEmbeddingQueryDucksemanticsJudgmentParserDucksemanticsPromptRunnerDucksemanticsScalarTextDucksemanticsSqlIdentifierDucksemanticsTableDucksemanticsTokenEmbeddingBatchDucksemanticsTokenEmbeddingProviderDucksemanticsTokenEmbeddingQuery

Dependencies:DBIS7s7contract

Readme and manuals

Help Manual

Help pageTopics
Annotate text against the semantic alias indexducksemantics_annotate
Judge mentions with a BebeLM/Rbebelm agentducksemantics_bebel_judge
Create a BebeLM prompt runnerducksemantics_bebel_runner
Create a BebeLM tool-call judgment parserducksemantics_bebel_tool_judgment_parser
Run a grounding benchmarkducksemantics_benchmark
Define benchmark casesducksemantics_benchmark_cases
Compute benchmark precision and recallducksemantics_benchmark_metrics
Cache a source fileducksemantics_cache_file
Cache an R value on diskducksemantics_cache_rds
Materialize transitive edge closureducksemantics_closure_sql
Cluster embedding rowsducksemantics_cluster_embeddings
Create a native ColBERT token-vector providerducksemantics_colbert_provider
Construct a ColBERT late-interaction queryducksemantics_colbert_query
Connect to a DuckDB semantic storeducksemantics_connect
Default judgment instructionsducksemantics_default_judgment_instructions
Cache provider embeddings in durable chunksducksemantics_embed_cached
Construct an embedding batchducksemantics_embedding_batch
Compare embedding clusters with graph edgesducksemantics_embedding_cluster_graph_agreement
Construct an embedding clustering specificationducksemantics_embedding_cluster_spec
Summarize stored embedding clustersducksemantics_embedding_cluster_summary
Construct an embedding index specificationducksemantics_embedding_index_spec
Wrap an embedding function as a typed embedding providerducksemantics_embedding_provider
Construct an embedding search queryducksemantics_embedding_query
Search embeddings with DuckDB vector functionsducksemantics_embedding_search
Create an EmbeddingGemma dense retrieval providerducksemantics_embeddinggemma_provider
Build the lexical alias indexducksemantics_index_aliases
Summarize semantic index sizeducksemantics_index_stats
Initialize semantic graph tablesducksemantics_init
Create the default JSON judgment parserducksemantics_json_judgment_parser
Judge mentions with a model runnerducksemantics_judge
Build a semantic judgment promptducksemantics_judgment_prompt
Search token embeddings with exact late interactionducksemantics_late_interaction_search
Create the default DuckDB lexical annotatorducksemantics_lexical_annotator
Materialize a fixed-dimension embedding tableducksemantics_materialize_embedding_index
Normalize text for semantic groundingducksemantics_normalize
Project any edge-shaped source relation into graph shapeducksemantics_projection_sql
Wrap a prompt function as a typed prompt runnerducksemantics_prompt_runner
Provider interface genericsducksemantics_embed ducksemantics_ground ducksemantics_parse ducksemantics_provider_generics ducksemantics_run ducksemantics_token_embed
Read an OBO ontology into semantic graph rowsducksemantics_read_obo
Record semantic judgmentsducksemantics_record_judgments
DuckDB semantic graph schemaducksemantics_schema_sql
Semantic graph table namesducksemantics_tables
Construct a token embedding batchducksemantics_token_embedding_batch
Construct a token embedding batch from a providerducksemantics_token_embedding_batch_from_provider
Wrap a token embedding function as a typed token providerducksemantics_token_embedding_provider
Construct a token embedding late-interaction queryducksemantics_token_embedding_query
Tokenize text for semantic groundingducksemantics_tokens
Store an embedding batch in DuckDBducksemantics_write_embeddings
Write graph rows into the semantic storeducksemantics_write_graph
Write an OBO ontology into the semantic storeducksemantics_write_obo
Store token embeddings for late-interaction scoringducksemantics_write_token_embeddings
Structural interface for text annotatorsDucksemanticsAnnotator
DBI connection referenceDucksemanticsDbConnection
Embedding batch for the semantic storeDucksemanticsEmbeddingBatch
Embedding clustering specificationDucksemanticsEmbeddingClusterSpec
Embedding index specificationDucksemanticsEmbeddingIndexSpec
Embedding matrix contractDucksemanticsEmbeddingMatrix
Structural interface for embedding providersDucksemanticsEmbeddingProvider
Embedding search queryDucksemanticsEmbeddingQuery
Structural interface for judgment parsersDucksemanticsJudgmentParser
Structural interface for prompt runnersDucksemanticsPromptRunner
Non-empty scalar textDucksemanticsScalarText
SQL identifierDucksemanticsSqlIdentifier
Data frame contractDucksemanticsTable
Token embedding batch for late-interaction storageDucksemanticsTokenEmbeddingBatch
Structural interface for token embedding providersDucksemanticsTokenEmbeddingProvider
Token embedding late-interaction queryDucksemanticsTokenEmbeddingQuery