somesci_dataset / README.md
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metadata
dataset_info:
  - config_name: default
    features:
      - name: id
        dtype: string
      - name: text
        dtype: string
      - name: tokens
        sequence: string
      - name: start_offsets
        sequence: uint32
      - name: labels
        sequence:
          class_label:
            names:
              '0': O
              '1': B-PROGRAMMINGENVIRONMENT
              '2': I-PROGRAMMINGENVIRONMENT
              '3': B-SOFTWARECOREFERENCE
              '4': I-SOFTWARECOREFERENCE
              '5': B-APPLICATION
              '6': I-APPLICATION
              '7': B-PLUGIN
              '8': I-PLUGIN
              '9': B-OPERATINGSYSTEM
              '10': I-OPERATINGSYSTEM
              '11': B-ALTERNATIVENAME
              '12': I-ALTERNATIVENAME
              '13': B-URL
              '14': I-URL
              '15': B-ABBREVIATION
              '16': I-ABBREVIATION
              '17': B-LICENSE
              '18': I-LICENSE
              '19': B-CITATION
              '20': I-CITATION
              '21': B-VERSION
              '22': I-VERSION
              '23': B-EXTENSION
              '24': I-EXTENSION
              '25': B-RELEASE
              '26': I-RELEASE
              '27': B-DEVELOPER
              '28': I-DEVELOPER
      - name: software
        sequence:
          - name: name
            dtype: string
          - name: type
            dtype: string
          - name: alternativename
            dtype: string
          - name: url
            sequence: string
          - name: abbreviation
            sequence: string
          - name: license
            sequence: string
          - name: citation
            sequence: string
          - name: version
            sequence: string
          - name: extension
            sequence: string
          - name: release
            sequence: string
          - name: developer
            sequence: string
    splits:
      - name: test
        num_bytes: 10731426
        num_examples: 97
    download_size: 3467360
    dataset_size: 10731426
  - config_name: plos_methods
    features:
      - name: id
        dtype: string
      - name: text
        dtype: string
      - name: tokens
        sequence: string
      - name: start_offsets
        sequence: uint32
      - name: labels
        sequence:
          class_label:
            names:
              '0': O
              '1': B-PROGRAMMINGENVIRONMENT
              '2': I-PROGRAMMINGENVIRONMENT
              '3': B-SOFTWARECOREFERENCE
              '4': I-SOFTWARECOREFERENCE
              '5': B-APPLICATION
              '6': I-APPLICATION
              '7': B-PLUGIN
              '8': I-PLUGIN
              '9': B-OPERATINGSYSTEM
              '10': I-OPERATINGSYSTEM
              '11': B-ALTERNATIVENAME
              '12': I-ALTERNATIVENAME
              '13': B-URL
              '14': I-URL
              '15': B-ABBREVIATION
              '16': I-ABBREVIATION
              '17': B-LICENSE
              '18': I-LICENSE
              '19': B-CITATION
              '20': I-CITATION
              '21': B-VERSION
              '22': I-VERSION
              '23': B-EXTENSION
              '24': I-EXTENSION
              '25': B-RELEASE
              '26': I-RELEASE
              '27': B-DEVELOPER
              '28': I-DEVELOPER
      - name: software
        sequence:
          - name: name
            dtype: string
          - name: type
            dtype: string
          - name: alternativename
            dtype: string
          - name: url
            sequence: string
          - name: abbreviation
            sequence: string
          - name: license
            sequence: string
          - name: citation
            sequence: string
          - name: version
            sequence: string
          - name: extension
            sequence: string
          - name: release
            sequence: string
          - name: developer
            sequence: string
    splits:
      - name: test
        num_bytes: 19566214
        num_examples: 480
    download_size: 5865285
    dataset_size: 19566214
  - config_name: plos_sentences
    features:
      - name: id
        dtype: string
      - name: text
        dtype: string
      - name: tokens
        sequence: string
      - name: start_offsets
        sequence: uint32
      - name: labels
        sequence:
          class_label:
            names:
              '0': O
              '1': B-PROGRAMMINGENVIRONMENT
              '2': I-PROGRAMMINGENVIRONMENT
              '3': B-SOFTWARECOREFERENCE
              '4': I-SOFTWARECOREFERENCE
              '5': B-APPLICATION
              '6': I-APPLICATION
              '7': B-PLUGIN
              '8': I-PLUGIN
              '9': B-OPERATINGSYSTEM
              '10': I-OPERATINGSYSTEM
              '11': B-ALTERNATIVENAME
              '12': I-ALTERNATIVENAME
              '13': B-URL
              '14': I-URL
              '15': B-ABBREVIATION
              '16': I-ABBREVIATION
              '17': B-LICENSE
              '18': I-LICENSE
              '19': B-CITATION
              '20': I-CITATION
              '21': B-VERSION
              '22': I-VERSION
              '23': B-EXTENSION
              '24': I-EXTENSION
              '25': B-RELEASE
              '26': I-RELEASE
              '27': B-DEVELOPER
              '28': I-DEVELOPER
      - name: software
        sequence:
          - name: name
            dtype: string
          - name: type
            dtype: string
          - name: alternativename
            dtype: string
          - name: url
            sequence: string
          - name: abbreviation
            sequence: string
          - name: license
            sequence: string
          - name: citation
            sequence: string
          - name: version
            sequence: string
          - name: extension
            sequence: string
          - name: release
            sequence: string
          - name: developer
            sequence: string
    splits:
      - name: test
        num_bytes: 526571
        num_examples: 677
    download_size: 155526
    dataset_size: 526571
  - config_name: pubmed_fulltext
    features:
      - name: id
        dtype: string
      - name: text
        dtype: string
      - name: tokens
        sequence: string
      - name: start_offsets
        sequence: uint32
      - name: labels
        sequence:
          class_label:
            names:
              '0': O
              '1': B-PROGRAMMINGENVIRONMENT
              '2': I-PROGRAMMINGENVIRONMENT
              '3': B-SOFTWARECOREFERENCE
              '4': I-SOFTWARECOREFERENCE
              '5': B-APPLICATION
              '6': I-APPLICATION
              '7': B-PLUGIN
              '8': I-PLUGIN
              '9': B-OPERATINGSYSTEM
              '10': I-OPERATINGSYSTEM
              '11': B-ALTERNATIVENAME
              '12': I-ALTERNATIVENAME
              '13': B-URL
              '14': I-URL
              '15': B-ABBREVIATION
              '16': I-ABBREVIATION
              '17': B-LICENSE
              '18': I-LICENSE
              '19': B-CITATION
              '20': I-CITATION
              '21': B-VERSION
              '22': I-VERSION
              '23': B-EXTENSION
              '24': I-EXTENSION
              '25': B-RELEASE
              '26': I-RELEASE
              '27': B-DEVELOPER
              '28': I-DEVELOPER
      - name: software
        sequence:
          - name: name
            dtype: string
          - name: type
            dtype: string
          - name: alternativename
            dtype: string
          - name: url
            sequence: string
          - name: abbreviation
            sequence: string
          - name: license
            sequence: string
          - name: citation
            sequence: string
          - name: version
            sequence: string
          - name: extension
            sequence: string
          - name: release
            sequence: string
          - name: developer
            sequence: string
    splits:
      - name: test
        num_bytes: 10731426
        num_examples: 97
    download_size: 3467360
    dataset_size: 10731426
configs:
  - config_name: default
    data_files:
      - split: test
        path: data/test-*
  - config_name: plos_methods
    data_files:
      - split: test
        path: plos_methods/test-*
  - config_name: plos_sentences
    data_files:
      - split: test
        path: plos_sentences/test-*
  - config_name: pubmed_fulltext
    data_files:
      - split: test
        path: pubmed_fulltext/test-*

SoMeSci Dataset

SoMeSci dataset is a dataset of software mentions in scientific papers. This dataset was converted from the original GitHUB repository SoMeSci.

The original upload is containing some documents without content. These documents are removed from this dataset.

Configurations

This dataset is available in three configurations that corresponds to original SoMeSci subsets:

  • pubmed_fulltext (default)
  • plos_methods
  • plos_sentences

Fields description

All configurations contain the following fields:

  • id: The unique identifier of the example. Corresponds to sample file name in the original dataset.

  • text: The text of the paragraph or the full text of the paper.

  • tokens: Tokenized text for which the labels are provided.

  • start_offsets: The start character offsets of the tokens in the text.

  • labels: The labels of the tokens. The labels are in the BIO format:

    • 0: O
    • 1: B-PROGRAMMINGENVIRONMENT
    • 2: I-PROGRAMMINGENVIRONMENT
    • 3: B-SOFTWARECOREFERENCE
    • 4: I-SOFTWARECOREFERENCE
    • 5: B-APPLICATION
    • 6: I-APPLICATION
    • 7: B-PLUGIN
    • 8: I-PLUGIN
    • 9: B-OPERATINGSYSTEM
    • 10: I-OPERATINGSYSTEM
    • 11: B-ALTERNATIVENAME
    • 12: I-ALTERNATIVENAME
    • 13: B-URL
    • 14: I-URL
    • 15: B-ABBREVIATION
    • 16: I-ABBREVIATION
    • 17: B-LICENSE
    • 18: I-LICENSE
    • 19: B-CITATION
    • 20: I-CITATION
    • 21: B-VERSION
    • 22: I-VERSION
    • 23: B-EXTENSION
    • 24: I-EXTENSION
    • 25: B-RELEASE
    • 26: I-RELEASE
    • 27: B-DEVELOPER
    • 28: I-DEVELOPER
  • software: Document level software mentions. Contains the following fields:

    • name
    • type
    • alternativename
    • url
    • abbreviation
    • license
    • citation
    • version
    • extension
    • release
    • developer

    Disambiguation is done on lexical level. Meaning that two software names are considered different if they have different normalized forms.