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--- |
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license: mit |
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language: |
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- en |
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tags: |
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- biology |
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- protein structure |
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- token classification |
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configs: |
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- config_name: protein_structure_NER_model_v3.1 |
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data_files: |
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- split: train |
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path: "annotation_IOB/train.tsv" |
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- split: dev |
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path: "annotation_IOB/dev.tsv" |
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- split: test |
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path: "annotation_IOB/test.tsv" |
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--- |
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## Overview |
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This data was used to train model: |
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https://huggingface.co/PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v3.1 |
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There are 20 different entity types in this dataset: |
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"bond_interaction", "chemical", "complex_assembly", "evidence", "experimental_method", "gene", |
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"mutant", "oligomeric_state", "protein", "protein_state", "protein_type", "ptm", "residue_name", |
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"residue_name_number","residue_number", "residue_range", "site", "species", "structure_element", |
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"taxonomy_domain" |
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The data prepared as IOB formated input has been used during training, develiopment |
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and testing. Additional data formats such as JSON and XML as well as CSV files are |
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also available and are described below. |
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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 | 717 | 709 | 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 | 1000 | 998 | 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 | 1441 | 1441 | 264 | |
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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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| PMC4918759 | 803 | 803 | 175 | |
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| PMC4855620 | 563 | 563 | 122 | |
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| PMC4822050 | 1521 | 1521 | 249 | |
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| PMC4822561 | 367 | 366 | 84 | |
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| PMC4885502 | 577 | 577 | 97 | |
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| PMC4746701 | 1130 | 1130 | 245 | |
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| PMC4820378 | 733 | 733 | 170 | |
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| PMC4773095 | 1323 | 1323 | 252 | |
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| PMC4857006 | 1358 | 1358 | 249 | |
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| PMC4774019 | 532 | 530 | 117 | |
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| total | 40254 | 40149 | 8042 | |
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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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* all.tsv --> all sentences and annotations used to create model |
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"PDBEurope/BiomedNLP-PubMedBERT-ProteinStructure-NER-v3.1"; 8042 sentences |
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* train.tsv --> training subset of the data; 5629 sentences |
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* dev.tsv --> development subset of the data; 1206 sentences |
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* test.tsv --> testing subset of the data; 1207 sentences |
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The total number of annotations is: 40149 |
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## Annotations in BioC JSON |
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The BioC formated JSON files of the publications have been downloaded from the annotation |
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tool TeamTat. The files are found in the directory: "annotated_BioC_JSON" |
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There is one file for each document and they follow standard naming |
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"unique PubMedCentral ID"_ann.json |
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Each document JSON contains the following relevant keys: |
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* "sourceid" --> giving the numerical part of the unique PubMedCentral ID |
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* "text" --> containing the complete raw text of the publication as a string |
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* "denotations" --> containing a list of all the annotations for the text |
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Each annotation is a dictionary with the following keys: |
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* "span" --> gives the start and end of the annotatiom span defined by sub keys: |
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* "begin" --> character start position of annotation |
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* "end" --> character end position of annotation |
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* "obj" --> a string containing a number of terms that can be separated by ","; the order |
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of the terms gives the following: entity type, reference to ontology, annotator, |
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time stamp |
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* "id" --> unique annotation ID |
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Here an example: |
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```json |
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[{"sourceid":"4784909", |
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"sourcedb":"", |
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"project":"", |
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"target":"", |
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"text":"", |
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"denotations":[{"span":{"begin":24, |
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"end":34}, |
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"obj":"chemical,CHEBI:,melaniev@ebi.ac.uk,2023-03-21T15:19:42Z", |
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"id":"4500"}, |
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{"span":{"begin":50, |
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"end":59}, |
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"obj":"taxonomy_domain,DUMMY:,melaniev@ebi.ac.uk,2023-03-21T15:15:03Z", |
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"id":"1281"}] |
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} |
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] |
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``` |
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## Annotations in BioC XML |
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The BioC formated XML files of the publications have been downloaded from the annotation |
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tool TeamTat. The files are found in the directory: "annotated_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_ann.xml |
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The key XML tags to be able to visualise the annotations in TeamTat as well as extracting |
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them to create the training data are "passage" and "offset". The "passage" tag encloses a |
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text passage or paragraph to which the annotations are linked. "Offset" gives the passage/ |
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paragraph offset and allows to determine the character starting and ending postions of the |
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annotations. The tag "text" encloses the raw text of the passage. |
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Each annotation in the XML file is tagged as below: |
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* "annotation id=" --> giving the unique ID of the annotation |
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* "infon key="type"" --> giving the entity type of the annotation |
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* "infon key="identifier"" --> giving a reference to an ontology for the annotation |
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* "infon key="annotator"" --> giving the annotator |
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* "infon key="updated_at"" --> providing a time stamp for annotation creation/update |
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* "location" --> start and end character positions for the annotated text span |
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* "offset" --> start character position as defined by offset value |
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* "length" --> length of the annotation span; sum of "offset" and "length" creates |
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the end character position |
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Here is a basic example of what the BioC XML looks like. Additional tags for document |
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management are not given. Please refer to the documenttation to find out more. |
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```xml |
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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE collection SYSTEM "BioC.dtd"> |
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<collection> |
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<source>PMC</source> |
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<date>20140719</date> |
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<key>pmc.key</key> |
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<document> |
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<id>4784909</id> |
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<passage> |
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<offset>0</offset> |
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<text>The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle</text> |
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<annotation id="4500"> |
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<infon key="type">chemical</infon> |
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<infon key="identifier">CHEBI:</infon> |
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<infon key="annotator">melaniev@ebi.ac.uk</infon> |
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<infon key="updated_at">2023-03-21T15:19:42Z</infon> |
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<location offset="24" length="10"/> |
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<text>Coenzyme A</text> |
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</annotation> |
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</passage> |
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</document> |
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</collection> |
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``` |
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## Annotations in CSV |
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The annotations and the relevant sentences they have been found in have also been made |
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available as tab-separated CSV files, one for each publication in the dataset. The files can |
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be found in directory "annotation_CSV". Each file is named as "unique PubMedCentral ID".csv. |
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The column labels in the CSV files are as follows: |
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* "anno_start" --> character start position of the annotation |
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* "anno_end" --> character end position of the annotation |
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* "anno_text" --> text covered by the annotation |
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* "entity_type" --> entity type of the annotation |
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* "sentence" --> sentence text in which the annotation was found |
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* "section" --> publication section in which the annotation was found |
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## Annotations in JSON |
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A combined JSON file was created only containing the relevant sentences and associated |
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annotations for each publication in the dataset. The file can be found in directory |
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"annotation_JSON" under the name "annotations.json". |
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The following keys are used: |
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* "PMC4850273" --> unique PubMedCentral of the publication |
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* "annotations" --> list of dictionaries for the relevant, annotated sentences of the |
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document; each dictionary has the following sub keys |
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* "sid" --> unique sentence ID |
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* "sent" --> sentence text as string |
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* "section" --> publication section the sentence is in |
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* "ner" --> nested list of annotations; each sublist contains the following items: |
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start character position, end character position, annotation text, |
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entity type |
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Here is an example of a sentence and its annotations: |
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```json |
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{"PMC4850273": {"annotations": |
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[{"sid": 0, |
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"sent": "Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont", |
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"section": "TITLE", |
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"ner": [ |
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[24,34,"Xyloglucan","chemical"], |
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[62,67,"Human","species"],] |
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},] |
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}} |
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``` |
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