Bionlp dataset. Important Dates for BioNLP Workshop Shared Task 1A .
Bionlp dataset The experiments are performed on the BioNLP Protein coreference dataset and CRAFT-CR dataset . This dataset can be viewed as an additional test for the MedNLI data created for the BioNLP 2019 shared task. The GENIA event extraction (GENIA) task is a main task in BioNLP Shared Task 2011 (BioNLP-ST '11). Automate any workflow Packages. It was created with a controlled search on MEDLINE. ©2021 Association for Computational Linguistics 64 emrKBQA: A Clinical Knowledge-Base Question Answering Dataset Preethi Raghavan1,3,*, Diwakar Mahajan1,3,#, Jennifer Liang1,3,x, Rachita Chandra1,3,y, Peter Szolovits2,3,z 1IBM Research, 2MIT CSAIL, 3MIT-IBM Watson AI Lab SpanMarker with bert-base-uncased on BioNLP2004 This is a SpanMarker model trained on the BioNLP2004 dataset that can be used for Named Entity Recognition. The phase II testing dataset will be released on April 12th (Friday), 2024. 3 Volume: Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing Month: July Year: 2020 Address: Online the PubMed corpus including 14,446,243 PubMed abstracts and the CORD-19 dataset, a collection of over 45,000 research papers focused on COVID-19 research. 2024. This page provides access to data collections created to support research in consumer-health question answering, extraction of adverse drug reactions, extraction of information from MEDLINE ® /PubMed ® citations, and many other Lister Hill National Center for Biomedical Communications, U. Registration opens: January 13th, 2023; Releasing of training and validation data: January 13th, 2023; Releasing of test data: April 13th, 2023 2021. Version 1. Participants can use available external resources, including, but not limited to medical QA datasets and question focus & type recognition datasets. These NLP applications, or tasks, are reliant on the availability of domain-specific language models (LMs) that are trained on a massive amount of data. Reload to refresh your session. The 22nd BioNLP workshop associated with the ACL SIGBIOMED special interest group is co-located with ACL 2023. Shared task on Large-Scale Radiology Report @article {vaya2020bimcv, title = {BIMCV COVID-19+: a large annotated dataset of RX and CT images from COVID-19 patients}, author = {Vay{\'a}, Maria De La Iglesia and Saborit, Jose Manuel and Montell In the quest to unravel the intricate mechanisms underlying tumors, understanding cancer is crucial for developing effective treatments. This project compiled information on each dataset, including task type, data scale, task description, and relevant data links. 17 Volume: Proceedings of the 21st Workshop on Biomedical Language Processing Month: May Year: 2022 Address: Dublin, Ireland Editors: Dina Demner-Fushman, Kevin Bretonnel Cohen, Sophia Ananiadou, Junichi Tsujii Our dataset also enhances the NER performance when combined with existing data, For each dataset_name, zero- and few-shot prompts are also provided in the benchmarks/{dataset_name}/ directory. You switched accounts on another tab or window. They start with "0" that makes every id field in a dataset unique. 2020. Posted by Irene January 10, 2019 November 15, 2019 Posted in Natural Language Processing, Resource. This paper introduces the approach of VPAI_Lab team’s experiments on BioNLP 2022 shared task 1 Medical Video EBM-NLP annotates PICO (Participants, Interventions, Comparisons and Outcomes) spans in clinical trial abstracts. Model Details Model Description Model Type: SpanMarker Encoder: bert-base-uncased Maximum 2020. 18653/v1 The BioNLP workshop associated with the ACL SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. 67–75. This dataset is composed of a set of titles and abstracts, extracted from scientific papers focusing on the rice species, and Our ultimate goal is to offer a shared task of rice gene/protein name recognition through the BioNLP Open Shared Tasks framework using the dataset, to facilitate an open comparison and evaluation of Proceedings of the BioNLP 2020 workshop , pages 140 149 Online, July 9, 2020 c 2020 Association for Computational Linguistics 140 BIOMRC: A Dataset for Biomedical Machine Reading Comprehension Petros Stavropoulos1,2, Dimitris Pappas1,2, Ion Androutsopoulos1, Ryan McDonald3,1 1Department of Informatics, Athens University of Economics and Business, %0 Conference Proceedings %T Towards Automatic Curation of Antibiotic Resistance Genes via Statement Extraction from Scientific Papers: A Benchmark Dataset and Models %A Chandak, Sidhant %A Zhang, Liqing %A Brown, Connor %A Huang, Lifu %Y Demner-Fushman, Dina %Y Cohen, Kevin Bretonnel %Y Ananiadou, Sophia %Y Tsujii, BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions. Data Instances; Data Fields; Data Splits; Dataset Creation. However, the main drawback is that these datasets are still manually labeled, BioNLP dataset, including BioNLP11EPI (Kim et al. Resources for BioNLP: datasets and tools. Common Units of Measure - Subset of the Unified Code for Units of Measure. Participation to the task was open to the academia This is a code reprository for the BioNLP 2021 paper emrKBQA: A Clinical Knowledge-Base Question Answering Dataset. py for the training script. Successful 'BioNLP Shared Task' published in 'Encyclopedia of Systems Biology' As shown in Table 1, the theme or themes of all events are considered primary arguments, that is, arguments that are critical to identifying the event. Use the Meta preprocessing configurations in all_preprocessing_configs. Contents. Curation Rationale; Source Data; Annotations; Personal and Sensitive Information; Considerations for Using the Data. (LREC 2016). Currently, the dataset only contains the samples in the training, validation, and phase I testing dataset. Abstract. 1 IMPORTANT DATES; 2 VISA Information; 3 Poster size: A Dataset and Benchmark for Low-Carb Diet The abundance of biomedical text data coupled with advances in natural language processing (NLP) is resulting in novel biomedical NLP (BioNLP) applications. Dataset Summary; Supported Tasks and Leaderboards; Languages; Dataset Structure. For regulation events, the entity or event stated as the cause of the regulation is also regarded as a primary argument. Navigation Menu Toggle navigation. , trained on both datasets). Lives_in relations which link a Microorganism entity to a location (either a Habitat or a Geographical entity) Exhibits relations which link Microorganism entity to a Phenotype entity. National Library of Medicine (NLM) projects. ; document_id should be a dataset provided document id. We’re on a journey to advance and democratize artificial intelligence BioNLP2004 NER dataset formatted in a part of TNER project. The sub task here is to find the relationship between the BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III). py shows how to preprocess the Genia dataset. We are excited to announce the new edition of the Shared Task on on Clinical Text generation at BioNLP 2024, co-located with ACL 2024. We then use the BioLaySum summarization dataset to evaluate the effects of different grounding sources on summary quality. md: this file; LICENSE: JNLBPA data license The BioNLP Shared Task series represents a community-wide move in bio-textmining toward fine-grained information extraction (IE). You signed out in another tab or window. Proceedings of the 23rd Workshop on Biomedical Natural Language Processing 80 papers; 2023. Jin et al. Here, we rely on preexisting datasets because they have Over 39 million published research papers in Computer Science, Neuroscience, and Biomedical. "PICO Element Detection in Medical Text via Long Short-Term Memory Neural Networks. 13 Volume: Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing Month: July Year: 2020 Address: Online The Evidence Inference dataset was recently released to facilitate research toward this end. Important Dates for BioNLP Workshop Shared Task 1A . *OVERVIEW* Utilize the MIMIC-IV dataset to automate the "Brief Hospital Course" & "Discharge Instructions" sections. Please check this page for more updates 2024. This task entails inferring the comparative performance of two treatments, with respect to a 2023. Proceedings of BioNLP Shared Task 2011 Workshop, pages 1–6, Portland, Oregon, USA, 24 June, 2011. Sign in Product Actions. The scientific literature on cancer is enormous, and our understanding of the molecular mechanisms of cancer is developing rapidly: a PubMed query for "cancer" returns 2. PubMed comprises more than 29 million BioNLP-ST 2013 broadens the scope of the text-mining application domains in biology by introducing new issues on cancer genetics and pathway curation. c 2011 Association for Computational Linguistics Overview of BioNLP Shared Task 2011 Jin-Dong Kim Database Center for Life Science 2-11-16 Yayoi, Bunkyo-ku, Tokyo jdkim@dbcls. An overview of the datasets is provided in the following figure. Preprocessing data for Meta. TAC dataset consists of 20 articles (reference articles) and citing art- icles that vary from 12 to 20 for each of the reference articles. The goal of the supporting resources for the BioNLP Shared Task 2016 is to provide the task participants with annotations from state-of-the-art automated tools in order to minimize the time-investment necessary to participate in the shared task and to allow for BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III). @InProceedings{peng2019transfer, author = {Yifan Peng and Shankai Yan and Zhiyong Lu}, title = {Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets}, booktitle = {Proceedings of the 2019 Workshop on Biomedical Natural Language Processing (BioNLP 2019)}, year = {2019}, pages Download Table | Statistics of BioNLP-ST 2013 GE dataset from publication: Optimizing graph-based patterns to extract biomedical events from the literature | In BioNLP-ST 2013 We participated in Original dataset released. Addressing this lacuna, our study introduces a comprehensive BioNLP instruction dataset, curated with limited human intervention. BioNLP-ST 2013 broadens the scope of the text-mining application domains in biology by introducing new issues on cancer genetics and pathway processing are provided to the participants in the form of analyses created by various state-of-the art tools on the dataset texts. , BioNLP 2020) ACL. Complete guidelines given to annotators can be seen here. - GitHub - ncbi-nlp/bluebert: BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III). BioNER. This repository contains tools and resources related to the corpus of the 2004 BioNLP / JNLPBA shared task. 2018. Among these, there are 38 Chinese datasets covering 10 BioNLP tasks and 131 English datasets covering 12 BioNLP tasks. json (3mb) Readme. Thomas Searle, Zina Ibrahim, and Richard Dobson. First, BioNLP primarily annotates the coreferential links among pro-tein/gene noun phrases, pronouns, and determiners. PubMed PubMed comprises more than 29 million citations for biomedical literature from MEDLINE, life science journals, and online books. You signed in with another tab or window. Moreover, we are going to combine NER and rule-based matching to extract the drug names and dosages reported in each transcription. </abstract> <identifier type="citekey">yuan-etal-2021-improving</identifier> <identifier type="doi">10. From this search 2,000 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. 0: This is the initial release for the BioNLP Workshop 2023 Shared Task 1A: Problem List Summarization. document) level. - bluebert/README. Named entity recognition (NER) is the [02/20/2024]: Shared task at BioNLP@ACL2024 online . This SpanMarker model uses bert-base-uncased as the underlying encoder. (2017) Deep learning for extracting protein–protein interactions from biomedical literature. For instance, one-shot for pubmedqa has the following information: TASK: Your task is to answer biomedical questions using the given abstract. The dataset and scripts for generating data will be released as part of a community-shared task on clinical KB-QA. Skip to content. TurkuNLP. It is one of the projects of the BioNLP initiative by the Center for Repository to track the progress in Biomedical Natural Language Processing (BioNLP), including the datasets and the current state-of-the-art for the most common BioNLP tasks. The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks 70 papers; 2022. If not provided in the dataset, it can be set equal to the upper level BioNLP Venue ID: bionlp. BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora. The task setup and data have since served as the basis of numerous studies and published event extraction For BioNLP-OST 2019, we introduced a new mental health informatics task called “RDoC Task”, Non-availability of RDoC labelled dataset and tedious labelling process hinders the use of RDoC framework to reach its full potential in Biomedical research community and Healthcare industry. From our experiments, we conclude that Pegasus is the best-performing model on the dataset, achieving a ROUGE-L F1 score of 0. ac. md at master · ncbi-nlp/bluebert For training data, teams can utilize the publicly available PLABA dataset , which comprises 750 abstracts, each manually adapted to plain language by at least one annotator, for a total of 7,643 sentence pairs. The task setup and data have since served as the basis of numerous studies and published event extraction Training Data: The MeQSum Dataset of consumer health questions and their summaries [2] could be used for training. e. Proceedings of the 21st Workshop on Biomedical Language Processing 44 papers; The BioNLP workshop, associated with the ACL SIGBIOMED special interest group, is an established primary venue for presenting research in language processing and language understanding for the biological and medical domains. %A Mahajan, Diwakar %A Chandra, Rachita %A Szolovits, Peter %Y Demner-Fushman, Dina %Y Cohen, Kevin Bretonnel %Y Ananiadou, Sophia %Y Tsujii, Junichi %S Proceedings of the 20th Workshop on BioNLP ACL'24 Shared Task on Streamlining Discharge Documentation View Challenge on Codabench (Update May 12, Participants are given a dataset based on MIMIC-IV which includes 109,168 visits to the Emergency Department (ED), split into training, validation, phase I testing, Biomedical LLM, A Bilingual (Chinese and English) Fine-Tuned Large Language Model for Diverse Biomedical Tasks - DUTIR-BioNLP/Taiyi-LLM the missing tailored instruction sets [16, 7]. Specifically, we introduceBioInstruct, a dataset comprising more than 25,000 natural language instructions along with their corresponding inputs and outputs. GitHub; The TurkuNLP Group is a group of researchers at the University of Turku as well as the UTU graduate school (UTUGS). id fields appear at the top (i. For some event types, further arguments The dataset is analyzed for semantics and the extent of copied text from human authored electronic health record (EHR) notes. We leverage the PubMed structured abstracts to create a biomedical aspect-based summarization dataset. Dataset, annotation guideline and baseline experiments for the PedSHAC corpora. Requirements; Dataset; Named entity recognition; Rule Download scientific diagram | A portion of the CFDK dataset in the BioNLP'11 shared task standoff format. We rst count the identical mentions in each document and nd that documents containing identical mentions Exceptional Bilingual BioNLP Multi-Task Capability in Chinese and English:Designing and constructing a bilingual Chinese-English instruction dataset (comprising over 1 million samples) for large model fine-tuning, enabling the model to excel in various BioNLP tasks including intelligent biomedical question-answering, doctor-patient dialogues, report generation, Version 1. Full dataset 36G, not restricted. The dataset of the CG task is based on an existing corpus composed of abstracts from After BioNLP-ST 2013 We explored three ways to further extend our event extraction system in our We construct BioRel, a large-scale dataset for biomedical relation extraction problem, (GE4) which is proposed in BioNLP 2016 Shared Task, BioNLP 2019 Shared Task, Footnote 1 Drug–Drug Interaction (DDI) and Chemical Disease Relation (CDR). With the unchanged task definition, the purpose of running this task is to measure the progress of the community on the task. pdf. The PubMed Computed Authors dataset consists of disambiguated author names from PubMed, freely available via API queries and FTP downloads. Skip to the content. 20 Volume: Proceedings of the 20th Workshop on Biomedical Language Processing Further analysis on a collected probing dataset shows that our model has better ability to model medical knowledge. Modalities: Text Dataset Card for BioNLP 2011 ID The dataset of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. make statistics on the identical mentions of the BioNLP dataset [6] and CRAFT-CR dataset [7]. 1,548 Consumer Health Questions submitted to NLM, For more information on this dataset, see Kilicoglu et al. ; question_id should be a dataset provided question id. In CRAFT, there are 97 full papers extracted from PMC, covering a broader range of coreferences. In: BioNLP 2017, Association for Computational Linguistics, Vancouver, Canada, pp. In the first iteration of CXR-LT held in 2023, we expanded upon the MIMIC-CXR dataset by enlarging the set of target classes from 14 to 26, generating labels for 12 new rare disease findings by parsing radiology reports. Exceptional Bilingual BioNLP Multi-Task Capability in Chinese and English:Designing and constructing a bilingual Chinese-English instruction dataset (comprising over 1 million samples) for large model fine-tuning, enabling the model to excel in various BioNLP tasks including intelligent biomedical question-answering, doctor-patient dialogues, report generation, This test set consists of 405 premise-hypothesis pairs curated by the same clinicians who worked on creating the original MedNLI dataset. Most of the existing domain-specific LMs adopted To access the Challenge dataset, participants should first register for the shared task through the BioNLP Workshop 2023 website [4]. 23 Volume: Proceedings of the 23rd Workshop on Biomedical Natural Language Processing Month: August Year: 2024 Address: Bangkok, Thailand To gauge the quantitative efficacy of our approach by assessing both precision and recall, we manually annotate a dataset provided by the Macula and Retina Institute. Dataset. 36 terminal classes were used to annotate the GENIA corpus. This dataset is now obsolete. Using advanced AI algorithms, the PubMed Computed Authors disambiguated more Image features of OpenI datasets (test) extracted using ConvNeXt-L model. 2008-March 2009), attracted wide attention, with 24 teams submitting final results. Additionally, the organizers may further update this dataset throughout the shared task to address issues raised by the participants. In addition to the dataset, we provide an example script for loading the dataset. To build and maintain comprehensive, up-to-date knowledge bases on cancer genetics, automatic support The BioNLP Shared Task series represents a community-wide move in bio-textmining toward fine-grained information extraction (IE). A last overview paper is dedicated to the preparation of these supporting resources. Schema Notes. For instance, the CHQs Dataset [3] contains additional annotations (e. Host and manage packages Security. Here we are going to see how to use scispaCy NER models to identify drug and disease names mentioned in a medical transcription dataset. g. It also builds on BioNLP-Corpora is a repository of biologically and linguistically annotated corpora and biological datasets. medical entities, question focus, question Shared task on Large-Scale Radiology Report Generation @ BioNLP ACL’24. 2013), comes from the Biomedical Natural Language Processing Workshops. For the GENIA task, the task definition remains the same as BioNLP Shared Task 2009 (BioNLP-ST'09). Table of Contents. Social Impact of Dataset The models and framework used in the BioNLP 2023 paper titled "Comparing and combining some popular NER approaches on Biomedical tasks" can be found here ! . This directory contains JNLPBA corpus data in standoff format and tools for recreating this data from the TAB-separated BIO format in which the corpus is distributed. In Proceedings of the BioNLP Shared Task 2013 Workshop, Association for Computational Linguistics, Sofia, Bulgaria, pp. The first event, the BioNLP 2009 shared task (Dec. In our previous experiment with T5, we used special tokens "<Assessment>", "<Subjective>" and "<Objective>" to indicate the input sections. See train. , 2003). from publication: Compressor Fault Diagnosis Knowledge: A Benchmark Dataset for Knowledge JNLPBA is a biomedical dataset that comes from the GENIA version 3. 2011) and BioNLP3GE dataset (Nédellec et al. The workshop has been running every year since 2002 and continues getting stronger. BioNLP2004 dataset contains training and test only, so we randomly sample a half size of test instances from the training set We uploaded some datasets that are ready to be used with the NCBI BlueBERT codes. The premises in this dataset do not have an overlap with the premises in MedNLI. Proceedings of the BioNLP 2021 workshop , pages 64 73 June 11, 2021. We created the BioInstruct, comprising 25,005 instructions to instruction AbstractIn this paper, we present a pipeline approach for the BioCreative VIII BioRED (Biomedical Relation Extraction Dataset) Track. rois. Peng Y. S. This ACL-BioNLP 2019 shared task is motivated by a need to develop relevant methods, techniques and gold standards for inference and entailment in the medical domain and their application to improve domain specific IR and QA systems NLI: The MedNLI dataset including 14,049 clinical sentence pairs [1]. Find and fix vulnerabilities Codespaces This dataset is introduced by Jin, Di, and Peter Szolovits. CHQA Named Entity Dataset . 0. Note that submissions can be generated from either 2 separate summarization models (i. The corresponding PICO Extraction task aims to identify the spans in clinical trial abstracts that describe the respective PICO elements. provided to the participants in the form of analyses created by various state-of-the art tools on the dataset texts. We also present a novel unsupervised method of reducing workload and cognitive bias. Citation Information @inproceedings{pyysalo-etal-2011-overview, title = "Overview of the Infectious Diseases ({ID}) task of {B}io{NLP} Shared Task 2011", author = "Pyysalo, Sampo and Ohta, Tomoko and Rak, Rafal and BioNLP-ST 2013 follows the general outline and goals of the previous tasks. In this project, Cancer-Alterome, addresses this challenge by presenting a literature-mined dataset focusing on the regulatory events within an organism's biological processes or clinical phenotypes induced by genetic alterations. BigScience Biomedical Datasets 121. Simplify the data access process. A For the shared task on large-scale radiology report generation at BioNLP@ACL2024. data. 45 Volume: The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks Month: July Year: 2023 X-rays. CHQA Named Entity Dataset. , Lu Z. We're thrilled to introduce BioInstruct—a dataset enhancing LLMs like Llama with 25,000+ tailored instructions for biomedical tasks. Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset (Searle et al. py to prepare data for Meta. If not provided in the dataset, it can be set equal to the top level id. 7 million scientific article citations, with 140,000 citations regarding "cancer" from 2011. Check out the new iteration of the Bacteria Biotope in BioNLP Open Shared Tasks 2019. The main focus of our research are various aspects of natural language processing / language technology and digital linguistics, ranging from corpus annotation and analysis to machine learning theory and applications. " Proceedings of the BioNLP 2018 workshop. Our research shows remarkable gains in question answering (QA), information extraction (IE), and text generation. 02 corpus (Kim et al. 💡 Motivation We curated the "Interpret-CXR" dataset for the following motivations: For the shared task on large-scale radiology report generation at BioNLP@ACL2024. Our approach combines fine-tuned PubMedBERT models for named entity recognition (NER), relation extraction (RE), and novelty detection (ND), with an entity linking (EL) approach based on PubTator and BERN2 models. Standardize the benchmark for future research in this field; 🎬 Get Started 🔬 Exciting breakthrough in BioNLP! 🧬. Dataset Card for JNLPBA Table of Contents Dataset Description. /preprocess. For BioNLP, we use the scorer Original dataset released. 2022. Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset. [ 9 ] trained biomedical ELMo (BioELMo) with PubMed abstracts and found features extracted by BioELMo contained entity-type and relational information relevant to the %0 Conference Proceedings %T BioELECTRA:Pretrained Biomedical text Encoder using Discriminators %A Kanakarajan, Kamal raj %A Kundumani, Bhuvana %A Sankarasubbu, Malaikannan %Y Demner Go to the bioNLP resource page . , one trained on each dataset) or a single unified model (i. In The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, pages 611–619, Toronto, Canada. To palliate these two limitations, we propose a radiology report summarization (RadSum) challenge on i) a new dataset of eleven different modalities and anatomies pairs based on the MIMIC-III In this paper, we elaborate on our approach for the shared task 1A issued by BioNLP Workshop 2023 titled Problem List Summarization. 2744 on the test dataset To overcome this limitation, BioNLP researchers have trained LMs on biomedical and clinical corpus and proved its effectiveness on various downstream tasks in BioNLP tasks [8–15]. Contents: README. bionlp-1. BioNLP 2023 Shared Task 1A focusses on generating a list of diagnoses and problems from the provider’s progress BIONLP 2023 and Shared Tasks @ ACL 2023. The BioNLP / JNLPBA Shared Task 2004 involves the identification and classification of technical terms referring to concepts of interest to biologists in the domain of molecular biology. 29–38. View PDF HTML (experimental) Abstract: To enhance the performance of large language models (LLMs) in biomedical natural language processing (BioNLP) by introducing a domain-specific instruction dataset and examining its impact when combined with multi-task learning principles. 1. jp Sampo Pyysalo University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo %0 Conference Proceedings %T emrKBQA: A Clinical Knowledge-Base Question Answering Dataset %A Raghavan, Preethi %A Liang, Jennifer J. - uw-bionlp/PedSHAC. . The BioNLP Protein Coreference dataset consists of 1210 PubMed abstracts and mainly focuses on protein/gene coreference. vfqy wcrxe qaia gypuqp ojfrrw ecpnct suw wnbqr tikv ncypn