Building a Corpus from Files and APIs

Bring your own relational data (recommended)

If your data is already tabular – a manual tracker, an institutional export, a spreadsheet of works – the most robust entry point is sm_corpus_from_tables(). It validates the required columns, coerces types, fills missing optional tables with correctly-typed 0-row tibbles, and returns a ready sm_corpus, side-stepping format-specific parsers entirely. A works-only corpus is perfectly valid:

works <- data.frame(
  work_id = paste0("W", 1:3),
  title = c("Spatial transcriptomics in cancer",
            "Immune checkpoint resistance",
            "A biomarker discovery cohort"),
  year = c("2019", "2020", "2021"),   # character -> coerced to integer
  doi = paste0("10.1234/example.", 1:3),
  cited_by_count = c(12, 5, 1)
)
corpus <- sm_corpus_from_tables(list(works = works))
#> ℹ works: coerced column year and cited_by_count to the schema type.
#> ℹ works: filled missing column abstract, type, source_id, oa_status, language,
#>   pmid, arxiv_id, openalex_id, is_retracted, retraction_date, and
#>   last_refreshed with typed `NA`.
corpus
#> 
#> ── <sm_corpus> ─────────────────────────────────────────────────────────────────
#> Works: 3 | Authors: 0 | Institutions: 0
#> Years: 2019 - 2021
#> Sources (journals): 0
#> Embeddings: none
#> Status: Unlocked (last refreshed: never)

You can pass any of works, authorships, sources, institutions, references, concepts, etc. as named list elements.

Materialising cached enrichment

Once you have a corpus, fold cached enrichment (a metrics table, a citation cache, …) into it with sm_materialise() rather than hand-writing the join. It matches by key, fills NA cells (or replaces with overwrite = TRUE), and returns a schema-valid corpus — avoiding the classic bind_rows() bug where a NULL element silently becomes a logical column.

metrics <- data.frame(work_id = corpus$works$work_id,
                      cnci = c(1.4, 0.8, 1.1))
corpus <- sm_materialise(corpus, sources = list(works = metrics))
#> ✔ Materialised 3 enrichment rows into works (+1 column).
"cnci" %in% names(corpus$works)
#> [1] TRUE

File ingestion

scimapR reads 12 bibliographic formats with native clean-room parsers.

# List available example files
sm_example_files()
#>  [1] "example_affiliation_postcode.csv"    
#>  [2] "example_dimensions.csv"              
#>  [3] "example_journal_index.csv"           
#>  [4] "example_lens.csv"                    
#>  [5] "example_openalex_inverted.json"      
#>  [6] "example_openalex.json"               
#>  [7] "example_pubmed.xml"                  
#>  [8] "example_realuse_affiliation_dict.csv"
#>  [9] "example_realuse_corpus.rds"          
#> [10] "example_realuse_reference.csv"       
#> [11] "example_ror.csv"                     
#> [12] "example_scopus.csv"                  
#> [13] "example_self_citation_corpus.rds"    
#> [14] "example_sparse.bib"                  
#> [15] "example_wos.txt"                     
#> [16] "example.bib"                         
#> [17] "example.ris"

# Read a BibTeX file
bib_path <- sm_example_files("example.bib")
corpus_bib <- sm_read_bib(bib_path)
#> ℹ Reading BibTeX file:
#>   '/tmp/RtmpPAHkFS/Rinst1de117df6e59/scimapR/extdata/example.bib'
#> ℹ Parsed 3 BibTeX entries.
print(corpus_bib)
#> 
#> ── <sm_corpus> ─────────────────────────────────────────────────────────────────
#> Works: 3 | Authors: 9 | Institutions: 0
#> Years: 2022 - 2024
#> Sources (journals): 2
#> Embeddings: none
#> Provenance: bibtex (3)
#> Status: Unlocked (last refreshed: never)

# Read an RIS file
ris_path <- sm_example_files("example.ris")
corpus_ris <- sm_read_ris(ris_path)
#> ℹ Reading RIS file:
#>   '/tmp/RtmpPAHkFS/Rinst1de117df6e59/scimapR/extdata/example.ris'
#> ℹ Parsed 3 RIS records.
nrow(corpus_ris$works)
#> [1] 3

Combining multiple sources

combined <- sm_build_corpus(corpus_bib, corpus_ris, dedupe = TRUE)
#> ℹ Re-keyed 3 works, 0 authors, 0 sources and 0 institutions in the second
#>   corpus.
#> ℹ 3 works share a DOI with the first corpus; use `sm_dedupe()` to remove
#>   duplicates.
#> ✔ Removed 3 duplicate works with the same doi.
nrow(combined$works)
#> [1] 3

Auto-detection

corpus_auto <- sm_read_auto(bib_path)
#> ℹ Detected format: "bibtex"
#> ℹ Reading BibTeX file:
#>   '/tmp/RtmpPAHkFS/Rinst1de117df6e59/scimapR/extdata/example.bib'
#> ℹ Parsed 3 BibTeX entries.
nrow(corpus_auto$works)
#> [1] 3

API fetching

For API-based ingestion, set your email for polite pool access:

Sys.setenv(SCIMAPR_MAILTO = "[email protected]")

# Fetch from OpenAlex
corpus <- sm_fetch_openalex(
 query = "spatial transcriptomics colorectal cancer",
 n_max = 100
)

All API fetchers populate the provenance table for reproducibility tracking.

Deduplication

corpus <- sm_example_corpus()
deduped <- sm_dedupe(corpus)

Validation

issues <- sm_validate(corpus)
nrow(issues)
#> [1] 0