entities.txt

[
  {
    "model": "en_ner_bionlp13cg_md",
    "entities": [
      {
        "name": "Cell",
        "type": "CELL"
      },
      {
        "name": "FOXA1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "condensed chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "Shao C(1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "J(2",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "Gao X(1",
        "type": "AMINO_ACID"
      },
      {
        "name": "L(4",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "Tumor",
        "type": "CANCER"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "CAS",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "CAS",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "CAS",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "Tumor",
        "type": "CANCER"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "CAS",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "Biomacromolecules",
        "type": "CANCER"
      },
      {
        "name": "DNA",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "nucleus",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "TFs",
        "type": "CELL"
      },
      {
        "name": "DNA",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "FOXA1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "TF",
        "type": "CELL"
      },
      {
        "name": "chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "FOXA1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "condensed chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "FOXA1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "IDRs",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "FOXA1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "condensed chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "FOXA1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "IDRs",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "FOXA1",
        "type": "GENE_OR_GENE_PRODUCT"
      },
      {
        "name": "chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "breast cancer cells",
        "type": "CELL"
      },
      {
        "name": "TFs",
        "type": "CELL"
      },
      {
        "name": "chromatin",
        "type": "CELLULAR_COMPONENT"
      },
      {
        "name": "DOI",
        "type": "CELLULAR_COMPONENT"
      }
    ],
    "sentences": [
      "1. Mol Cell. 2024 Jan 18;84(2):244-260.e7. doi: 10.1016/j.molcel.2023.11.020. Epub\n2023 Dec 14.",
      "\n\nFOXA1 forms biomolecular condensates that unpack condensed chromatin to function\nas a pioneer factor.",
      "\n\nJi D(1), Shao C(1), Yu J(2), Hou Y(3), Gao X(1), Wu Y(1), Wang L(4), Chen P(5).",
      "\n\nAuthor information:\n(1)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China.",
      "\n(2)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China.",
      "\n(3)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative\nBiology, School of Life Sciences, Central China Normal University, Wuhan 430079,\nChina.",
      "\n(4)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Beijing Frontier Research Center for Biological Structure, School\nof Life Sciences, Tsinghua University, Beijing 100084, China.",
      "Electronic\naddress: wanglian15@tsinghua.org.cn.",
      "\n(5)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for\nExcellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of\nSciences, Beijing 100101, China.",
      "Electronic address: chenping@ccmu.edu.cn.\n\nEukaryotic DNA is packaged into chromatin in the nucleus, restricting the\nbinding of transcription factors (TFs) to their target DNA sites.",
      "FOXA1\nfunctions as a pioneer TF to bind condensed chromatin and initiate the opening\nof local chromatin for gene expression.",
      "However, the principles of FOXA1\nrecruitment and how it subsequently unpacks the condensed chromatin remain\nelusive.",
      "Here, we revealed that FOXA1 intrinsically forms submicron-sized\ncondensates through its N- and C-terminal intrinsically disordered regions\n(IDRs).",
      "Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin.",
      "In\naddition, the DNA-binding capacity of FOXA1 contributes to its ability to both\nform condensates and dissolve condensed chromatin.",
      "Further genome-wide\ninvestigation showed that IDRs enable FOXA1 to bind and unpack the condensed\nchromatin to regulate the proliferation and migration of breast cancer cells.",
      "\nThis work provides a principle of how pioneer TFs function to initiate competent\nchromatin states using their IDRs.",
      "\n\nCopyright \u00a9 2023 Elsevier Inc. All rights reserved.",
      "\n\nDOI: 10.1016/j.molcel.2023.11.020\nPMID: 38101414 [Indexed for MEDLINE]\n\nConflict of interest statement: Declaration of interests The authors declare no\ncompeting interests."
    ]
  },
  {
    "model": "en_ner_bc5cdr_md",
    "entities": [
      {
        "name": "Tumor",
        "type": "DISEASE"
      },
      {
        "name": "Tumor",
        "type": "DISEASE"
      },
      {
        "name": "breast cancer",
        "type": "DISEASE"
      }
    ],
    "sentences": [
      "1. Mol Cell. 2024 Jan 18;84(2):244-260.e7. doi: 10.1016/j.molcel.2023.11.020. Epub\n2023 Dec 14.",
      "\n\nFOXA1 forms biomolecular condensates that unpack condensed chromatin to function\nas a pioneer factor.",
      "\n\nJi D(1), Shao C(1), Yu J(2), Hou Y(3), Gao X(1), Wu Y(1), Wang L(4), Chen P(5).",
      "\n\nAuthor information:\n(1)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China.",
      "\n(2)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China.",
      "\n(3)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative\nBiology, School of Life Sciences, Central China Normal University, Wuhan 430079,\nChina.",
      "\n(4)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Beijing Frontier Research Center for Biological Structure, School\nof Life Sciences, Tsinghua University, Beijing 100084, China.",
      "Electronic\naddress: wanglian15@tsinghua.org.cn.",
      "\n(5)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for\nExcellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of\nSciences, Beijing 100101, China.",
      "Electronic address: chenping@ccmu.edu.cn.\n\nEukaryotic DNA is packaged into chromatin in the nucleus, restricting the\nbinding of transcription factors (TFs) to their target DNA sites.",
      "FOXA1\nfunctions as a pioneer TF to bind condensed chromatin and initiate the opening\nof local chromatin for gene expression.",
      "However, the principles of FOXA1\nrecruitment and how it subsequently unpacks the condensed chromatin remain\nelusive.",
      "Here, we revealed that FOXA1 intrinsically forms submicron-sized\ncondensates through its N- and C-terminal intrinsically disordered regions\n(IDRs).",
      "Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin.",
      "In\naddition, the DNA-binding capacity of FOXA1 contributes to its ability to both\nform condensates and dissolve condensed chromatin.",
      "Further genome-wide\ninvestigation showed that IDRs enable FOXA1 to bind and unpack the condensed\nchromatin to regulate the proliferation and migration of breast cancer cells.",
      "\nThis work provides a principle of how pioneer TFs function to initiate competent\nchromatin states using their IDRs.",
      "\n\nCopyright \u00a9 2023 Elsevier Inc. All rights reserved.",
      "\n\nDOI: 10.1016/j.molcel.2023.11.020\nPMID: 38101414 [Indexed for MEDLINE]\n\nConflict of interest statement: Declaration of interests The authors declare no\ncompeting interests."
    ]
  },
  {
    "model": "en_ner_jnlpba_md",
    "entities": [
      {
        "name": "FOXA1",
        "type": "PROTEIN"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "pioneer factor",
        "type": "PROTEIN"
      },
      {
        "name": "Wuhan 430079,\nChina",
        "type": "CELL_LINE"
      },
      {
        "name": "Eukaryotic DNA",
        "type": "DNA"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "transcription factors",
        "type": "PROTEIN"
      },
      {
        "name": "target DNA sites",
        "type": "DNA"
      },
      {
        "name": "TF",
        "type": "PROTEIN"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "FOXA1",
        "type": "PROTEIN"
      },
      {
        "name": "N-",
        "type": "PROTEIN"
      },
      {
        "name": "IDRs",
        "type": "CELL_LINE"
      },
      {
        "name": "FOXA1",
        "type": "PROTEIN"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "FOXA1",
        "type": "PROTEIN"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "IDRs",
        "type": "PROTEIN"
      },
      {
        "name": "FOXA1",
        "type": "PROTEIN"
      },
      {
        "name": "chromatin",
        "type": "DNA"
      },
      {
        "name": "breast cancer cells",
        "type": "CELL_TYPE"
      }
    ],
    "sentences": [
      "1. Mol Cell. 2024 Jan 18;84(2):244-260.e7. doi: 10.1016/j.molcel.2023.11.020. Epub\n2023 Dec 14.",
      "\n\nFOXA1 forms biomolecular condensates that unpack condensed chromatin to function\nas a pioneer factor.",
      "\n\nJi D(1), Shao C(1), Yu J(2), Hou Y(3), Gao X(1), Wu Y(1), Wang L(4), Chen P(5).",
      "\n\nAuthor information:\n(1)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China.",
      "\n(2)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China.",
      "\n(3)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative\nBiology, School of Life Sciences, Central China Normal University, Wuhan 430079,\nChina.",
      "\n(4)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Beijing Frontier Research Center for Biological Structure, School\nof Life Sciences, Tsinghua University, Beijing 100084, China.",
      "Electronic\naddress: wanglian15@tsinghua.org.cn.",
      "\n(5)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for\nExcellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of\nSciences, Beijing 100101, China.",
      "Electronic address: chenping@ccmu.edu.cn.\n\nEukaryotic DNA is packaged into chromatin in the nucleus, restricting the\nbinding of transcription factors (TFs) to their target DNA sites.",
      "FOXA1\nfunctions as a pioneer TF to bind condensed chromatin and initiate the opening\nof local chromatin for gene expression.",
      "However, the principles of FOXA1\nrecruitment and how it subsequently unpacks the condensed chromatin remain\nelusive.",
      "Here, we revealed that FOXA1 intrinsically forms submicron-sized\ncondensates through its N- and C-terminal intrinsically disordered regions\n(IDRs).",
      "Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin.",
      "In\naddition, the DNA-binding capacity of FOXA1 contributes to its ability to both\nform condensates and dissolve condensed chromatin.",
      "Further genome-wide\ninvestigation showed that IDRs enable FOXA1 to bind and unpack the condensed\nchromatin to regulate the proliferation and migration of breast cancer cells.",
      "\nThis work provides a principle of how pioneer TFs function to initiate competent\nchromatin states using their IDRs.",
      "\n\nCopyright \u00a9 2023 Elsevier Inc. All rights reserved.",
      "\n\nDOI: 10.1016/j.molcel.2023.11.020\nPMID: 38101414 [Indexed for MEDLINE]\n\nConflict of interest statement: Declaration of interests The authors declare no\ncompeting interests."
    ]
  },
  {
    "model": "en_ner_craft_md",
    "entities": [
      {
        "name": "Cell",
        "type": "CL"
      },
      {
        "name": "FOXA1",
        "type": "GGP"
      },
      {
        "name": "Genetic",
        "type": "SO"
      },
      {
        "name": "Eukaryotic DNA",
        "type": "CL"
      },
      {
        "name": "chromatin",
        "type": "GO"
      },
      {
        "name": "nucleus",
        "type": "GO"
      },
      {
        "name": "DNA sites",
        "type": "SO"
      },
      {
        "name": "FOXA1",
        "type": "GGP"
      },
      {
        "name": "chromatin",
        "type": "GO"
      },
      {
        "name": "gene",
        "type": "SO"
      },
      {
        "name": "FOXA1",
        "type": "GGP"
      },
      {
        "name": "chromatin",
        "type": "GO"
      },
      {
        "name": "FOXA1",
        "type": "GGP"
      },
      {
        "name": "regions",
        "type": "SO"
      },
      {
        "name": "FOXA1",
        "type": "GGP"
      },
      {
        "name": "FOXA1",
        "type": "GGP"
      },
      {
        "name": "FOXA1",
        "type": "GGP"
      },
      {
        "name": "chromatin",
        "type": "GO"
      },
      {
        "name": "breast cancer cells",
        "type": "CL"
      },
      {
        "name": "chromatin",
        "type": "GO"
      }
    ],
    "sentences": [
      "1. Mol Cell. 2024 Jan 18;84(2):244-260.e7. doi: 10.1016/j.molcel.2023.11.020. Epub\n2023 Dec 14.",
      "\n\nFOXA1 forms biomolecular condensates that unpack condensed chromatin to function\nas a pioneer factor.",
      "\n\nJi D(1), Shao C(1), Yu J(2), Hou Y(3), Gao X(1), Wu Y(1), Wang L(4), Chen P(5).",
      "\n\nAuthor information:\n(1)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China.",
      "\n(2)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China.",
      "\n(3)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Hubei Key Laboratory of Genetic Regulation and Integrative\nBiology, School of Life Sciences, Central China Normal University, Wuhan 430079,\nChina.",
      "\n(4)National Laboratory of Biomacromolecules, CAS Center for Excellence in\nBiomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing\n100101, China; Beijing Frontier Research Center for Biological Structure, School\nof Life Sciences, Tsinghua University, Beijing 100084, China.",
      "Electronic\naddress: wanglian15@tsinghua.org.cn.",
      "\n(5)Department of Immunology, School of Basic Medical Sciences, Beijing Key\nLaboratory for Tumor Invasion and Metastasis, Capital Medical University,\nBeijing 100069, China; National Laboratory of Biomacromolecules, CAS Center for\nExcellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of\nSciences, Beijing 100101, China.",
      "Electronic address: chenping@ccmu.edu.cn.\n\nEukaryotic DNA is packaged into chromatin in the nucleus, restricting the\nbinding of transcription factors (TFs) to their target DNA sites.",
      "FOXA1\nfunctions as a pioneer TF to bind condensed chromatin and initiate the opening\nof local chromatin for gene expression.",
      "However, the principles of FOXA1\nrecruitment and how it subsequently unpacks the condensed chromatin remain\nelusive.",
      "Here, we revealed that FOXA1 intrinsically forms submicron-sized\ncondensates through its N- and C-terminal intrinsically disordered regions\n(IDRs).",
      "Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin.",
      "In\naddition, the DNA-binding capacity of FOXA1 contributes to its ability to both\nform condensates and dissolve condensed chromatin.",
      "Further genome-wide\ninvestigation showed that IDRs enable FOXA1 to bind and unpack the condensed\nchromatin to regulate the proliferation and migration of breast cancer cells.",
      "\nThis work provides a principle of how pioneer TFs function to initiate competent\nchromatin states using their IDRs.",
      "\n\nCopyright \u00a9 2023 Elsevier Inc. All rights reserved.",
      "\n\nDOI: 10.1016/j.molcel.2023.11.020\nPMID: 38101414 [Indexed for MEDLINE]\n\nConflict of interest statement: Declaration of interests The authors declare no\ncompeting interests."
    ]
  }
]