Datasets:

jimmyzxj
/

drosophila-literature-corpus

pmcid stringlengths 8 11	title stringlengths 5 295	abstract stringlengths 0 3.31k	sections dict
PMC5540154	In vitro characterization of a novel Isu homologue from Drosophila melanogaster for de novo FeS-cluster formation	Model for mitochondrial Fe-S cluster assembly with bypass mechanisms for FeS mineral accumulation.	{ "INTRO": [ "INTRODUCTION", "FeS-cluster cofactors are ubiquitous in biology and play integral roles in nearly every biochemical pathway. In recent years, several human diseases have been linked to dysfunctional FeS-cluster metabolism, including Friedreich’s ataxia and IscU myopathy. Research at the molecula...
PMC7615346	An improved Erk biosensor detects oscillatory Erk dynamics driven by mitotic erasure during early development	Extracellular signal-regulated kinase (Erk) signaling dynamics elicit distinct cellular responses in a variety of contexts. The early zebrafish embryo is an ideal model to explore the role of Erk signaling dynamics in vivo, as a gradient of activated diphosphorylated Erk (P-Erk) is induced by fibroblast growth factor (...	{ "INTRO": [ "Introduction", "Embryonic development requires coordinated communication, proliferation, and movement of cells on a grand scale. The highly conserved extracellular signal-regulated kinase (Erk) is a key node connecting these processes and plays a critical role in coordinating cell fate specifica...
PMC11911433	Drosophila ovarian stem cell niche ageing involves coordinated changes in transcription and alternative splicing	Ageing is associated with alterations in gene expression and alternative splicing. Here, the authors show that ageing of the Drosophila ovarian stem cell niche involves coordinated changes in both expression and splicing, with distinct niche cells exhibiting specific ageing signatures.	{ "INTRO": [ "Introduction", "The healthy function of adult organs in animals requires controlled homeostasis during tissue maintenance or in response to pathophysiological situations. As a general principle, tissue function relies on populations of adult stem cells capable of making most of the cell types fo...
PMC3291507	A Screen for Round Egg Mutants in Drosophila Identifies Tricornered, Furry, and Misshapen as Regulators of Egg Chamber Elongation	The elongation of tissues and organs during embryonic development results from the coordinate polarization of cell behaviors with respect to the elongation axis. Within the Drosophila melanogaster ovary, initially spherical egg chambers lengthen dramatically as they develop to create the elliptical shape of the mature ...	{ "INTRO": [ "The lengthening of tissues and organs is a common theme in the development of multicellular organisms. This type of directional morphogenesis often requires that cell behaviors be coordinately polarized within the tissue plane and with respect to the elongation axis. The Frizzled/Strabismus and Fat/...
PMC4198113	" Drosophila Tribbles Antagonizes Insulin Signaling-Mediated Growth and Metabolism via Interactions (...TRUNCATED)	" Drosophila Tribbles (Trbl) is the founding member of the Trib family of kinase-like docking protei(...TRUNCATED)	{"INTRO":["Introduction","Tribbles (Trib) family members are found throughout the metazoan lineage a(...TRUNCATED)
PMC7655108	"Conditional protein tagging methods reveal highly specific subcellular distribution of ion channels(...TRUNCATED)	"Neurotransmitter receptors and ion channels shape the biophysical properties of neurons, from the s(...TRUNCATED)	{"INTRO":["Introduction","How neural circuits implement certain computations in order to process sen(...TRUNCATED)
PMC8864734	Parallel and population-specific gene regulatory evolution in cold-adapted fly populations	"Changes in gene regulation at multiple levels may comprise an important share of the molecular chan(...TRUNCATED)	{"INTRO":["Introduction","Different species or populations often evolve similar phenotypes when adap(...TRUNCATED)
PMC4402144	"Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced si(...TRUNCATED)	"Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologic(...TRUNCATED)	{"INTRO":["INTRODUCTION","Architectural proteins (also known as insulator proteins) facilitate conta(...TRUNCATED)
PMC12163413	Parkin mediates the mitochondrial dysfunction through mRpL18	"Loss of function of parkin leads to mitochondrial dysfunction, which is closely related to Parkinso(...TRUNCATED)	{"INTRO":["Parkinson’s disease (PD) is the second prevalent neurodegenerative movement disorder wh(...TRUNCATED)
PMC4617972	Regulation of alternative splicing in Drosophila by 56 RNA binding proteins	"Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA sequence e(...TRUNCATED)	{"INTRO":["Most metazoan genes contain introns that are removed from their primary transcripts (pre-(...TRUNCATED)

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Drosophila Literature Corpus

A corpus of full-text scientific articles from PubMed Central related to Drosophila melanogaster gene research.

Dataset Description

This corpus contains ~17,000 full-text scientific articles downloaded from the PubMed Central Open Access Subset via the BioC-PMC API. The articles are associated with genes that have expert-curated summaries in FlyBase.

Usage

from datasets import load_dataset

corpus = load_dataset("TODO/drosophila-literature-corpus")

# Access a document
doc = corpus["train"][0]
print(doc["pmcid"])
print(doc["title"])
print(doc["abstract"])
print(doc["sections"])  # Dict with keys: INTRO, METHODS, RESULTS, DISCUSS, CONCL

Dataset Structure

Each record contains:

Field	Type	Description
`pmcid`	string	PubMed Central ID
`title`	string	Article title
`abstract`	string	Article abstract
`sections`	dict	Mapping of section type to list of paragraphs

Section Types

INTRO - Introduction
METHODS - Methods/Materials
RESULTS - Results
DISCUSS - Discussion
CONCL - Conclusion

Dataset Statistics

Total documents: 16,898
Source: PubMed Central Open Access Subset
Format: BioC JSON (converted to JSONL)

Source

Articles were retrieved using the BioC-PMC API:

https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/{pmcid}/unicode

This corpus is part of the Drosophila Agent Benchmark, which evaluates AI agents on literature-based gene annotation tasks.

License

The articles in this corpus are from the PubMed Central Open Access Subset and are available under various Creative Commons licenses. Please refer to individual article licenses for specific terms.

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