Datasets:

boonyhow
/

plos-citation-contexts

paper_id stringlengths 28 28	journal stringclasses 12 values	title stringlengths 13 281	abstract stringlengths 0 5.95k	sections listlengths 0 338	references listlengths 0 810
10.1371/journal.pbio.0000001	plos_biology	A Functional Analysis of the Spacer of V(D)J Recombination Signal Sequences	During lymphocyte development, V(D)J recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS), which serves as the binding site for the recombination machinery. The murine Jβ2.6 gene segment is a recombinationally i...	[ { "label": "introduction", "heading": "Introduction", "text": "During B- and T-lymphocyte development, the immunoglobulin (Ig) and T-cell receptor (TCR) genes are assembled from discrete V, D, and J gene elements via a process of genomic rearrangements known as V(D)J recombination (Fugmann et al. 2000a;...	[ { "ref_id": "pbio-0000001-Akamatsu1", "label": "1", "doi": null, "pmid": null, "type": "journal", "authors": [ "Akamatsu Y", "Oettinger MA" ], "year": "1998", "title": "Distinct roles of RAG1 and RAG2 in binding the V(D)J recombination signal sequences.", "source"...
10.1371/journal.pbio.0000002	plos_biology	Viral Discovery and Sequence Recovery Using DNA Microarrays	Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterizatio...	[ { "label": "introduction", "heading": "Introduction", "text": "Over the past two decades, technological advances in molecular biology have fuelled progress in the discovery of new pathogens associated with human diseases. The identification of novel viruses such as hepatitis C virus (Choo et al. 1989), ...	[ { "ref_id": "pbio.0000002-Chang1", "label": "1", "doi": null, "pmid": null, "type": "journal", "authors": [ "Chang Y", "Cesarman E", "Pessin MS", "Lee F", "Culpepper J" ], "year": "1994", "title": "Identification of herpesvirus-like DNA sequences in ...
10.1371/journal.pbio.0000005	plos_biology	The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum	"Plasmodium falciparum is the causative agent of the most burdensome form of human malaria, affectin(...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"Human malaria is caused by four species of(...TRUNCATED)	[{"ref_id":"pbio-0000005-Afonso1","label":"1","doi":null,"pmid":null,"type":"journal","authors":["Af(...TRUNCATED)
10.1371/journal.pbio.0000006	plos_biology	"DNA Analysis Indicates That Asian Elephants Are Native to Borneo and Are Therefore a High Priority (...TRUNCATED)	"The origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are eit(...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"Elephants have a very limited distribution(...TRUNCATED)	[{"ref_id":"pbio-0000006-Andaya1","label":"1","doi":null,"pmid":null,"type":"book","authors":["Anday(...TRUNCATED)
10.1371/journal.pbio.0000010	plos_biology	The Roles of APC and Axin Derived from Experimental and Theoretical Analysis of the Wnt Pathway	"Wnt signaling plays an important role in both oncogenesis and development. Activation of the Wnt pa(...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"Considerable effort employing biochemistry(...TRUNCATED)	[{"ref_id":"pbio-0000010-Alon1","label":"1","doi":null,"pmid":null,"type":"journal","authors":["Alon(...TRUNCATED)
10.1371/journal.pbio.0000012	plos_biology	Genome-Wide RNAi of C. elegans Using the Hypersensitive rrf-3 Strain Reveals Novel Gene Functions	"RNA-mediated interference (RNAi) is a method to inhibit gene function by introduction of double-str(...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"RNA interference (RNAi) is targeted gene s(...TRUNCATED)	[{"ref_id":"pbio-0000012-Ashrafi1","label":"1","doi":null,"pmid":null,"type":"journal","authors":["A(...TRUNCATED)
10.1371/journal.pbio.0000013	plos_biology	Drosophila Free-Running Rhythms Require Intercellular Communication	"Robust self-sustained oscillations are a ubiquitous characteristic of circadian rhythms. These incl(...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"Circadian rhythms of diverse organisms are(...TRUNCATED)	[{"ref_id":"pbio-0000013-Allada1","label":"1","doi":null,"pmid":null,"type":"journal","authors":["Al(...TRUNCATED)
10.1371/journal.pbio.0000019	plos_biology	From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria	"The rapid increase in published genomic sequences for bacteria presents the first opportunity to re(...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"The availability of complete sequences of (...TRUNCATED)	[{"ref_id":"pbio-0000019-Akman1","label":"1","doi":null,"pmid":null,"type":"journal","authors":["Akm(...TRUNCATED)
10.1371/journal.pbio.0000020	plos_biology	"Candidate Gene Association Study in Type 2 Diabetes Indicates a Role for Genes Involved in β-Cell (...TRUNCATED)	"Type 2 diabetes is an increasingly common, serious metabolic disorder with a substantial inherited (...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"Type 2 diabetes is a serious metabolic dis(...TRUNCATED)	[{"ref_id":"pbio-0000020-Almind1","label":"1","doi":null,"pmid":null,"type":"journal","authors":["Al(...TRUNCATED)
10.1371/journal.pbio.0000021	plos_biology	Developmental Origin and Evolution of Bacteriocytes in the Aphid–Buchnera Symbiosis	"Symbiotic relationships between bacteria and insect hosts are common. Although the bacterial endosy(...TRUNCATED)	[{"label":"introduction","heading":"Introduction","text":"Endosymbiosis is common in insects, with m(...TRUNCATED)	[{"ref_id":"pbio-0000021-Baumann1","label":"1","doi":null,"pmid":null,"type":"book","authors":["Baum(...TRUNCATED)

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PLOS citation contexts

Full text of PLOS research articles with every in-text citation resolved to its sentence and (where the reference list provides one) the cited DOI. Built from the PLOS JATS XML corpus (allofplos).

Usage

from datasets import load_dataset
ds  = load_dataset("boonyhow/plos-citation-contexts")                    # all journals
one = load_dataset("boonyhow/plos-citation-contexts", "plos_one")        # a single journal

Follow a citation to its reference entry (works whether or not the DOI is known):

paper = ds["train"][0]
refs = {r["ref_id"]: r for r in paper["references"]}
for sec in paper["sections"]:
    for c in sec["citations"]:
        ref = refs.get(c["ref_id"])
        print(c["sentence"], "->", c["cited_doi"] or (ref and ref["raw"]))

Configs

config	papers
`all`	367,213
`plos_one`	310,503
`plos_neglected_tropical_diseases`	11,287
`plos_computational_biology`	10,930
`plos_pathogens`	10,258
`plos_genetics`	10,186
`plos_biology`	5,446
`plos_global_public_health`	3,444
`plos_medicine`	3,372
`plos_digital_health`	728
`plos_climate`	329
`plos_mental_health`	260
`plos_water`	257
`plos_sustainability_and_transformation`	104
`plos_complex_systems`	65
`plos_clinical_trials`	44

Schema

One row per paper.

field	description
`paper_id`	DOI of the citing paper
`journal`	PLOS journal (same as the config name)
`title`, `abstract`	article title and main abstract (structured abstracts as `Heading: text`)
`sections`	list of sections in document order (subsections are separate entries)
`references`	the paper's full reference list, in order

Each section: label (introduction / methods / results / discussion / other; subsections inherit their parent's label), heading, text (paragraphs joined by blank lines; figure/table captions excluded), and citations.

Each citation: sentence (the sentence containing the in-text marker), ref_id (key into references), and cited_doi (the reference's DOI, or null). A sentence citing several works appears once per cited work; citation ranges such as [3]–[6] are expanded.

Each reference: ref_id, label (as printed, e.g. 12), doi, pmid, type (journal / book / other ...), authors (Surname Initials), year, title (article or chapter title), source (journal or book title), volume, pages (page range or e-locator), and raw (a one-line formatted citation).

Notes

cited_doi / doi are null when the reference list doesn't give a DOI. This is common before ~2014, for books, and for web resources. The reference fields (title, first author, year, source) are enough to resolve most of these against Crossref, OpenAlex, or PubMed.
DOIs are lowercased and stripped of https://doi.org/ prefixes.
Only research-article items are included (no editorials, synopses, or corrections).
There is a single train split. If you split for evaluation, split by paper (not by citation row) to avoid leakage.

License

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