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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 | 1129 | 1129 | 205 |
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| PMC4784909 | 868 | 868 | 204 |
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| PMC4850288 | 718 | 710 | 146 |
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| PMC4887326 | 942 | 942 | 152 |
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| PMC4833862 | 1044 | 1044 | 192 |
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| PMC4832331 | 739 | 718 | 134 |
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| PMC4852598 | 1239 | 1228 | 250 |
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| PMC4786784 | 1573 | 1573 | 232 |
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| PMC4848090 | 1002 | 1000 | 192 |
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| PMC4792962 | 1297 | 1297 | 256 |
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| PMC4841544 | 1460 | 1459 | 274 |
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| PMC4772114 | 824 | 824 | 165 |
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| PMC4872110 | 1283 | 1283 | 250 |
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| PMC4848761 | 888 | 884 | 252 |
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| PMC4919469 | 1636 | 1624 | 336 |
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| PMC4880283 | 783 | 783 | 166 |
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| PMC4968113 | 1245 | 1245 | 292 |
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| PMC4937829 | 633 | 633 | 181 |
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| PMC4854314 | 498 | 488 | 139 |
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| PMC4871749 | 411 | 411 | 79 |
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| PMC4869123 | 922 | 922 | 195 |
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| PMC4888278 | 580 | 580 | 102 |
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| PMC4795551 | 1475 | 1475 | 297 |
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| PMC4831588 | 1087 | 1070 | 224 |
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| PMC4918766 | 1027 | 1027 | 210 |
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| PMC4802042 | 1445 | 1445 | 268 |
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| PMC4896748 | 2652 | 2638 | 480 |
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| PMC4781976 | 115 | 113 | 24 |
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| PMC4802085 | 983 | 983 | 193 |
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| PMC4887163 | 856 | 856 | 196|
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| total | 31354 | 31252 | 6286 |
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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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