Datasets:

OTAR3088
/

BioData-CL_Article-Sentences

PMCID string	Title string	Sentences string
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The infiltration of immune cells and their roles of the infiltrating-immune cells in gastrointestinal stromal tumor (GIST) is still unclear.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	We aimed to discover the infiltration cell types and the relationship between the infiltrating-immune cells and the progression of GIST.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Single-cell RNA sequencing were performed to discover types of the infiltrating-immune cells and to analyze CellChat between cells.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Immunohistochemistry of 80 GIST samples were used to clarify the relation between macrophages and recurrence risk.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	In vitro, flow cytometry and Real-time PCR were performed to uncover a potential mechanism of tumor cell regulation of macrophages.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Tumor cells, macrophages, and T-cells were the predominant cell types.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The MIF/CXCR4 axis was the most common ligand–receptor interaction between macrophages and tumor cells.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	As the risk increased, expression levels of CD68, CD206, MIF, and CXCR4 gradually increased.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	In vitro, we found that GIST882 was able to secrete MIF and GIST882 cell supernatant upregulated M2 polarization.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Real-time PCR showed that expression levels of IL-10 mRNA and Arginase-1 mRNA were also the highest in the GIST882 cell supernatant group.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	These findings identify that macrophages are the most abundant infiltrating cells in GIST.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The MIF/CXCR4 axis is the most common ligand–receptor interaction between macrophages and tumor cells.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	GIST cells can regulate macrophage M2 polarization through the MIF/CXCR4 axis.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumors in the gastrointestinal tract (1).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	It is well-known that GISTs originate from the interstitial cells of Cajal and that GISTs are characterized by acquired gene mutations.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Specifically, KIT (75–80%) and PDGFRA (5–10%) are the most common gain-of-function mutations (2, 3).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The risk stratification based on tumor size, tumor site, and mitotic count is often used to predict the recurrence risk.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Targeted therapy is the first choice for the patients with metastatic disease and those with intermediate or high recurrence risk (4).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Imatinib, from the first generation of tyrosine kinase inhibitors (TKIs), is the most effective drug.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	However, patients invariably develop drug resistance.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The second generation and the third generation of TKIs have limited benefit and more drug side effects (5).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Thus, it is important to develop new treatment strategies.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Recently, the monoclonal antibodies against immunological checkpoints PD-1 and CTLA-4 have been used in most tumors to improve overall survival (6–8).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	However, not all the patients can benefit from the immune therapy.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Factors such as PD-1/PD-L1, tumor mutational burden, and microsatellite instability have been suggested to predict treatment response.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Tumor-infiltrating immune cells seem to play an important role in treatment responses and tumor progression (9–11).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Available studies have shown abundant immune cell infiltration in GIST (5, 12–14).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Moreover, it has been demonstrated that imatinib could lead to the activation of CD8 T cells and that CD8 T cells also promote imatinib’s antitumor effects (5, 15).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	However, CD8 T cells become exhausted and macrophage count increases with tumor progression (12, 16).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Although abundant immune cell infiltration has been found in GIST microenvironment, clinical studies have shown that immunotherapy is not ideal (17, 18).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Thus, it is important to clarify the roles of infiltrated immune cells in the progression of GIST.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	In this study, we aimed to determine the role of macrophages during tumor progression and cell-chat types between macrophages and tumor cells.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Two patients (G01 and G02) were recruited for single-cell transcriptome analysis.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The two tumors were both located on the greater curvature of the gastric body.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The patient G01 underwent surgical resection, and the patient G02 underwent endoscopic resection.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Immunohistochemical results showed that CD117, DOG-1, and CD34 were positive.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The maximum tumor diameter in the patient G01 was 10 cm, and the mitotic index was 12/50 high-power fields (HPF).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Thus, the risk in G01 was considered high.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The maximum diameter of the tumor in the patient G02 was 2 cm, and the mitotic index was 1/50 HPF.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Hence, the risk in G02 was defined as very low.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Tumor tissues were obtained from the resection specimens and were cut into small pieces.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	These pieces were digested with collagenase IV for 15 min at 37°C.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Next, 70-µm cell strainer was used for filtration.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Countess II Automated Cell Counter was used to determine the cell viability.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells/µL (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification, and library construction were all performed as per the manufacturer’s protocol.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Qubit was used for library quantification before pooling.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The final library pool was sequenced on an Illumina NovaSeq 6000 instrument using 150-base-pair paired-end reads.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Cell ranger 3.0 software was used to generate cells × genes matrixes, and all parameters were set to default.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Criteria of quality control were as follows: (a) RNA counts less than 500; (b) RNA counts larger than 98% of cells; (c) mitochondrial gene expression percentage higher than 15%.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	A tool named CellChat was used to analyze and infer intercellular communication networks from these single-cell transcriptome data.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Tissue microarray with 5-micron was created from paraffin-embedded tumor tissues, which were collected from January 2011 to September 2020.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The inclusion criteria were as follows: (1) all patients were diagnosed with GIST; (2) Clinicopathological information were complete.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The exclusion criteria were as follows: (1) patients were treated with targeted drugs; (2) tumors were not located in stomach or intestine; (3) tissue was not used for immunohistochemistry.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	According to these inclusion criteria and exclusion criteria, 80 patients were included for this study.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Immunohistochemistry and immunofluorescence were performed on the tissue microarray with the following antibodies: rabbit polyclonal antibodies against human CD8 (ZEN Bio, Lot No:10011860), CD206 (Protein tech, Lot No:00080496), MIF (ZEN Bio, Lot No:20200101), and CXCR4 (ZEN Bio, Lot No: BJ10221968), and monoclonal mouse antibody against human CD68 (Abcam, Lot No:00098190).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	ImageJ software was used to scan the stained tissue chip and count the stained cells.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Human GIST cells GIST882 with a mutation in KIT exon 13 were provided by Jonathan Fletcher (Dana-Farber Cancer Institute, Boston, MA) (19, 20).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	GIST882 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, HyClone, Logan, UT) with high glucose supplemented with 10% fetal bovine serum (FBS, HyClone) and 1% penicillin/streptomycin (HyClone).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	GIST882 cells were identified as CD117-positive by flow cytometry.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Human THP-1 monocytes were kindly provided by Stem Cell Bank, Chinese Academy of Science.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	THP-1 monocytes were grown in RPMI 1640 (HyClone) supplemented with 10% FBS and 1% penicillin/streptomycin.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	THP-1 monocytes were treated with PMA (100 ng/mL, Sigma-Aldrich, MO, USA) to induce them to differentiate into macrophage-like cells (21).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	GIST882 cells were cultured to 60% confluence and replaced with FBS-free medium.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The supernatants were collected at 24 and 48 h and stored at −80°C.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The secreted MIF in GIST882 supernatants was quantified by ELISA (Beyotime Biotechnology, China) following standard protocols.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Human-specific antibodies (CD206, Lot No: B318421 and CD86, Lot No: 0209406) were purchased from BD Biosciences.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	All samples of these groups were measured by BD flow cytometry.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	FlowJo software (version 7.6) (Ashland, OR, USA) was used to analyze these data.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Total RNA was extracted from GIST882 cells by using TRIzol reagent (Takara Bio Inc., Japan) in accordance with the manufacturer’s instructions.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Total RNA (1 μg) was reversely transcribed to form cDNA using cDNA synthesis kit (Yeasen, China).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Real-time PCR was quantified using Hieff qPCR SYBR Green Master Mix Kit (Yeasen) and performed on iQ5 Opticon System (Bio-Rad, Hercules, CA).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The expression of mRNA was normalized to that of glyceraldehyde-3-phosphate dehydrogenase and calculated by using the 2 method.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The study protocol was approved by the Ethics Committee of Sichuan Cancer Hospital (SCCHEC-02-2021-013).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Written informed consent was obtained from the patients.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Patient records/information were anonymized, and the methods were adopted in accordance with the approved guidelines.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The Fisher exact test and the t test were used for comparison of different groups.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	These statistical analyses were conducted with the GraphPad Prism software version 9 and SPSS 26.0 (IBM SPSS).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	In the single-cell RNA sequencing analysis, we included one patient with very-low-risk GIST and one patient with high-risk GIST.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The clinicopathological characteristics are shown in Table 1 .
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	After quality control, 11 208 effective cells were obtained in the G01 sample (high risk), whereas 9 996 effective cells were obtained in the G02 sample (very low risk).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Clusters were detected and visualized by uniform manifold approximation and projection (UMAP) ( Figure 1 ).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The following cell clusters were identified in the samples: tumor cells, macrophages/monocytes, CD8 T cells, dendritic cells, endothelial cells, and NK cells.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Immune cells were the majority of the infiltrating cells in the two tumor samples ( Figure 2 ).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The major cell types were the same in the two tumor samples, namely tumor cells, macrophages/monocytes, and CD8 T cells.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	However, the counts of infiltrating cells differed between the two tumor samples ( Table 2 ).
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	In G01, the count of tumor cells was 6176, accounting for 55.1% of the total cell number; the count of macrophages was 3850, accounting for 34.3% of the total cell number; and the count of CD8 T cells was 700, accounting for 6.2% of the total cell number.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	In G02, the count of tumor cells was 2750, accounting for 27.5% of the total cell number; the count of macrophages was 4130, accounting for 41.3% of the total cell number; and the count of CD8 T cells was 1593, accounting for 15.9% of the total cell number.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	These results revealed that CD8 T cells were more abundant in the very-low-risk GIST sample than in the high-risk GIST sample.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	In contrast, macrophages were less abundant in the very-low-risk GIST sample than in the high-risk GIST sample.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Clinicopathological characteristics of two patients performed by single-cell RNA sequencing.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Cell clusters were visualized by uniform manifold approximation and projection (UMAP) in these two tumors.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Distribution of infiltration cells in two tumors.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	G01: high risk GIST; G02: very low risk GIST.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Cell counts of every cluster in two samples.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	Seven cell types were identified in the single-cell analysis.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	To further show the potential interactions between these cell types, CellChat was used to quantitatively infer and analyze cell-to-cell communication networks in tumor tissues.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The interaction numbers and interaction weights of cell-to-cell were analyzed in G01 and G02 as shown in Figure 3 .
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	The thicker lines showed more significant interaction between the cell clusters.
PMC11502962	Gastrointestinal stromal tumors regulate macrophage M2 polarization through the MIF/CXCR4 axis to immune escape	These results showed the high interaction strength of tumor cells with macrophages and monocytes.

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Dataset Card for Dataset Name

Dataset Description

Dataset Summary This dataset has been extracted from Europe PMC (EPMC), a free database offering comprehensive access to life sciences research literature. EPMC aggregates content from various sources, including PubMed, arXiv, and other repositories, and provides open access to millions of scientific articles. This dataset has been generated as part of a project collaboration between Europe PMC, Open Targets, and ChEMBL] at EMBL-EBI.

Dataset Details

The dataset focuses on mentions of cell lines and related entities in biomedical text, such as cell types, related disease mentions, genes proteins etc. This makes it a valuable resource as it can be used for(but not limited to) the following downstream natural language processing (NLP) tasks in the biomedical domain.

NLP Tasks

Named Entity Recognition (NER): Identify and classify mentions of cell lines or related entities appearing in biomedical contexts.
Relationship Extraction: Extract relationships between cell lines and other biomedical entities, such as genes, diseases, or drugs.
Text Classification: Classify sentences or articles based on their relevance to specific cell lines, particularly in cancer research or drug development.
Sentiment Analysis: Analyze the sentiment or tone of texts discussing cell lines, such as the evaluation of experimental results (positive or negative).
Information Retrieval: Develop systems to retrieve articles or specific mentions of cell lines based on user queries.
Entity Linking: Link cell line mentions in text to standardized identifiers in cell line ontologies or databases.
Question Answering (QA): Build systems that can answer specific questions about cell lines, such as their role in particular diseases or experiments.
Topic Modeling: Analyze the dataset to uncover major themes or trends in research involving cell lines.
Text Summarization: Automatically generate summaries of articles or sections discussing cell lines.

Who funded the creation of the dataset?

Any other comments?

The dataset aims to provide a foundational resource for advancing NLP in biomedicine.

Dataset Composition

What experiments were initially run on this dataset? No experiments have been conducted yet. Updates will follow as they occur.

Data Collection Process

How was the data collected? The dataset was collected using the Europe PMC API. Articles marked as "open access" were retrieved, and those labeled as "retraction of publication" were excluded. Duplicate entries were filtered by ensuring unique PMCIDs.
Who was involved in the data collection process? The data collection process was carried out by researchers at EMBL-EBI, leveraging automated tools for querying and processing the Europe PMC repository.
Are there any known errors, sources of noise, or redundancies in the data? None have been identified yet.

Data Preprocessing

What preprocessing/cleaning was done?

Only open-access articles were retrieved.
Articles labeled as "retraction of publication" were excluded.
Duplicate entries based on the PMCID column were removed.
Paragraph text from each section of an article was Extracted with the relevant section referenced in the 'Section Column'
Extra whitespace, inlne math/latex formatting and irrelevant sections such "Disclosure", "Publisher's note", etc, were filtered
Name identifiers and personal data was also removed from the dataset

Dataset Distribution

How is the dataset distributed? The dataset is freely available for use and reproduction. Proper citation of the authors is required(Information to be updated).
When will the dataset be released/first distributed? To be updated.

Dataset Maintenance

Who is supporting/hosting/maintaining the dataset?

Europe PMC, and ChEMBL team responsible for the dataset's maintenance.

How does one contact the owner/curator/manager of the dataset?

Contact can be made via the community discussion forums on GitHub or Hugging Face.

Will the dataset be updated?

Yes, updates will occur as the project progresses.

How often and by whom?

Updates will be carried out periodically by the team.

How will updates/revisions be documented and communicated?

Updates will be documented via GitHub, using version tags.

Is there a repository to link to any/all papers/systems that use this dataset?

Yes, a GitHub repository will track publications and systems using this dataset.

If others want to extend/augment/build on this dataset, is there a mechanism for them to do so?

Yes, contributions are encouraged via GitHub. Quality will be assessed through pull requests, and accepted contributions will be communicated to users via version tags and release notes.

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Collection including OTAR3088/BioData-CL_Article-Sentences

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Data produced relating to model train/test cycles which have been archived - due to data versioning or priorities changing • 6 items • Updated 5 days ago