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README.md
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Annotation was carried out with the free annotation tool TeamTat (https://www.teamtat.org/) and
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documents were downloaded as BioC XML before converting them to IOB, annotation only JSON and CSV format.
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Documents and annotations are easiest viewed by using the BioC XML files and opening
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them in free annotation tool TeamTat. More about the BioC
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format can be found here: https://bioc.sourceforge.net/
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## Annotations in IOB format
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The IOB formated files can be found in the directory: "annotation_IOB"
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The four files are as follows:
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Annotation was carried out with the free annotation tool TeamTat (https://www.teamtat.org/) and
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documents were downloaded as BioC XML before converting them to IOB, annotation only JSON and CSV format.
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The number of annotations and sentences in each file is given below:
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| document ID | number of annotations in BioC XML | number of annotations in IOB/JSON/CSV | number of sentences |
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| --- | --- | --- | --- |
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| PMC4850273 | 1121 | 1121 | 204 |
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| PMC4784909 | 865 | 865 | 204 |
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| PMC4850288 | 716 | 708 | 146 |
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| PMC4887326 | 933 | 933 | 152 |
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| PMC4833862 | 1044 | 1044 | 192 |
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| PMC4832331 | 739 | 718 | 134 |
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| PMC4852598 | 1229 | 1218 | 250 |
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| PMC4786784 | 1549 | 1549 | 232 |
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| PMC4848090 | 987 | 985 | 191 |
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| PMC4792962 | 1268 | 1268 | 256 |
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| PMC4841544 | 1434 | 1433 | 273 |
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| PMC4772114 | 825 | 825 | 166 |
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| PMC4872110 | 1276 | 1276 | 253 |
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| PMC4848761 | 887 | 883 | 252 |
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| PMC4919469 | 1628 | 1616 | 336 |
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| PMC4880283 | 771 | 771 | 166 |
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| PMC4937829 | 625 | 625 | 181 |
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| PMC4968113 | 1238 | 1238 | 292 |
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| PMC4854314 | 481 | 471 | 139 |
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| PMC4871749 | 383 | 383 | 76 |
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| total | 19999 | 19930 | 4095 |
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Documents and annotations are easiest viewed by using the BioC XML files and opening
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them in free annotation tool TeamTat. More about the BioC
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format can be found here: https://bioc.sourceforge.net/
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## Raw BioC XML files
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These are the raw, un-annotated XML files for the publications in the dataset in BioC format.
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The files are found in the directory: "raw_BioC_XML".
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There is one file for each document and they follow standard naming
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"unique PubMedCentral ID"_raw.xml.
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## Annotations in IOB format
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The IOB formated files can be found in the directory: "annotation_IOB"
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The four files are as follows:
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