BioNLP2021

This is the code repository for the paper Word-Level Alignment of Paper Documents with their Electronic Full-Text Counterparts

The repository contains code for converting both .nxml and .pdf files to MMAX2 format, and for creating an alignment between both representations.

For copyright reasons, we cannot provide the scanned .pdf documents from our collection, nor all of the corresponding .pdf or .nxml files from PubMed Central. Instead, the ./data folder contains the open-access paper

Seiya Watanabe, Yoshiaki Tanimoto, Seiji Yamauchi, Yuzuru Tozawa, Shigeki Sawayama, and Yasuo Watanabea (2014): Identification and characterization of trans-3-hydroxy-l-proline dehydratase and Δ1-pyrroline-2-carboxylate reductase involved in trans-3-hydroxy-l-proline metabolism of bacteria FEBS Open Bio. 2014; 4: 240–250.

in .pdf and .nxml format for demonstration. Note, however, that both conversion tools (pmc2mmax and pdf2mmax) can be run in bulk mode for converting entire folders of input documents at once. To use the bulk mode, provide paths (instead of files) to the respective command line parameters (see below).

For questions, you can contact Mark-Christoph Müller.

You can also create an issue, or start a discussion.

We are looking forward to hearing from you!

---

Setup

The alignment code uses the MMAX2 data format internally, so installing pyMMAX2 is required. Installing the Java-based MMAX2 annotation tool is only required for viewing the converted data, and is strongly recommended.

Also, the latest release version of tesseract (4.1.1) is required. tesseract is bundled by default with many Linuxes. Check you local version with tesseract --version! If you need to install tesseract 4.1.1, more infos can be found on the official tesseract page or here.

conda create -n bionlp2021 python=3.7
conda activate bionlp2021
git clone https://github.com/nlpAThits/BioNLP2021
cd BioNLP2021
pip install -r requirements.txt
git clone https://github.com/nlpAThits/pyMMAX2
pip install pyMMAX2/.
git clone https://github.com/nlpAThits/MMAX2

Convert sample PMC-NXML to MMAX2 Format

(bionlp2021) foo@bar:~$  python ./code/pmc2mmax.py --pmc_path ./data/nxml/PMC3958920.nxml --mmax2_base_path ./data/MMAX2/from_nxml/

Console output

Level file name set to PMC3958920_structure_markables.xml
Markables at ./data/MMAX2/from_nxml/./Markables/PMC3958920_structure_markables.xml not found, skipping!
Level file name set to PMC3958920_alignments_markables.xml
Markables at ./data/MMAX2/from_nxml/./Markables/PMC3958920_alignments_markables.xml not found, skipping!

MMAX2 Project Info:
-------------------
.mmax file        : ./data/MMAX2/from_nxml/PMC3958920.mmax
Basedata elements : 8532
Markable levels   :
 structure        :   506 markables [DEFAULT: none defined]
 alignments       :     0 markables [DEFAULT: none defined]

Open file in MMAX2 annotation tool

(This is optional.)

(bionlp2021) foo@bar:~$ cd MMAX2
(bionlp2021) foo@bar:~$ ./mmax2_flex.sh ../data/MMAX2/from_nxml/PMC3958920.mmax

Convert sample PDF to MMAX2 Format (via PNG)

Text recognition is done with tesseract 4.1.1 (via pytesseract). Use the required --tessdata_dir parameter to point tesseract to the language model to use. The following command expects the tessdata model at the provided path (you might have to adapt that to your system).

Alternative tesseract models can be downloaded here: tessdata_best. Download the folders to your system and point tesseract to them using the --tessdata_dir parameter. When trying different tesseract models, make sure to keep the --force_new_mmax2 option such that new OCR results will actually be created.

(bionlp2021) foo@bar:~$ python ./code/pdf2mmax.py --pdf_path ./data/pdf/real-pdf/PMC3958920.pdf  --mmax2_base_path ./data/MMAX2/from_png/converted/ --force_new_mmax2 --png_base_path ./data/temp_png/ --force_new_png --dpi 300 --tessdata_dir /usr/share/tesseract-ocr/4.00/tessdata

Console output

Level file name set to PMC3958920_ocr_words_level.xml
Markables at ./data/MMAX2/from_png/converted/Markables/PMC3958920_ocr_words_level.xml not found, skipping!
Level file name set to PMC3958920_ocr_lines_level.xml
Markables at ./data/MMAX2/from_png/converted/Markables/PMC3958920_ocr_lines_level.xml not found, skipping!
Level file name set to PMC3958920_alignments_markables.xml
Markables at ./data/MMAX2/from_png/converted/Markables/PMC3958920_alignments_markables.xml not found, skipping!
	Converting ./data/pdf/real-pdf/PMC3958920.pdf to 300 dpi PNG file ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...
	File ./data/temp_png//[email protected]
		OCR ...
		BS4 ...
		hOCR2MMAX2 ...

Open file in MMAX2 annotation tool (Optional)

(bionlp2021) foo@bar:~$ cd MMAX2
(bionlp2021) foo@bar:~$ ./mmax2_flex.sh ../data/MMAX2/from_png/converted/PMC3958920.mmax

Create a word-level alignment of the two documents

The following creates an alignment with all pre- and post-processing options (best) between the PNG-converted .pdf (conv) file and the .nxml file. The alignment is identified by the label best_conv.

(bionlp2021) foo@bar:~$ python ./code/align.py --ocr_mmax2_path ./data/MMAX2/from_png/converted/ --xml_mmax2_path ./data/MMAX2/from_nxml/ --alignment_label best_conv --de_hyphenate --pre_conflate --pre_split --post_forcealign

Console output

Level file name set to PMC3958920_ocr_words_level.xml
Level file name set to PMC3958920_ocr_lines_level.xml
Level file name set to PMC3958920_alignments_markables.xml
Markables at ./data/MMAX2/from_png/converted/Markables/PMC3958920_alignments_markables.xml not found, skipping!
Retrieving alignment markables with label 'best_conv' ...
Level file name set to PMC3958920_structure_markables.xml
Level file name set to PMC3958920_alignments_markables.xml
Markables at ./data/MMAX2/from_nxml/./Markables/PMC3958920_alignments_markables.xml not found, skipping!
Retrieving alignment markables with label 'best_conv' ...
Compressing, #words in A: 13617, #words in B: 8532
De-hyphenating...
Conflating...
Splitting...
48 pre-splits, recursing...
Splitting...
Force-aligning...

Result

The alignment information is added to the two aligned MMAX2 documents by means of markables on the alignment level of each document, such that a word in the .nxml-based document (left) is associated with a markable that has as its 'target' attribute the id of the aligned word in the converted .png document (right). When viewed in MMAX2, aligned words (=those with an associated alignment markable) are rendered in pink.

As can be seen, quite a few 'matching' words are aligned (rendered in pink, e.g. 'dehydratase') which should not be aligned. Some of these errors are likely due to forced alignment or other alignment heuristics.

Evaluation / Validation

Evaluation computes P, R, and F for the task of aligning words from the .nxml document to the corresponding image-based document. For details, please see our paper.

(bionlp2021) foo@bar:~$ python ./code/evaluate_alignment.py --ocr_mmax2_path ./data/MMAX2/from_png/converted/ --xml_mmax2_path ./data/MMAX2/from_nxml/ --alignment_label best_conv --eval_outfile eval_out.txt --add_validation

Console output

Level file name set to PMC3958920_ocr_words_level.xml
Level file name set to PMC3958920_ocr_lines_level.xml
Level file name set to PMC3958920_alignments_markables.xml
Level file name set to PMC3958920_structure_markables.xml
Level file name set to PMC3958920_alignments_markables.xml
File exists, creating backup ./data/MMAX2/from_nxml/./Markables/PMC3958920_alignments_markables.xml.1623133464353
File exists, creating backup ./data/MMAX2/from_png/converted/Markables/PMC3958920_alignments_markables.xml.1623133464377
best_conv: P, R, F: 0.9701711491442543	0.9301453352086263	0.9497367161321205

best_conv: P, R, F (micro): 0.9701711491442543	0.9301453352086263	0.9497367161321205 n = 1

Using the --add_validation parameter will label TP and FP cases in both documents. In MMAX2, these can be visualized as follows (just re-load the previously loaded files in MMAX2).

Words considered as TP are displayed in green, FP as red. Note that evaluation itself (details are given in the paper) is rather strict: The first words of the abstract (trans-4-Hydroxy-l-p) are considered as FP due to the mismatch in the left context, although the alignment is clearly correct.

For questions, you can contact Mark-Christoph Müller.

You can also create an issue, or start a discussion.

We are looking forward to hearing from you!