1. What is pygetpapers

Research Papers right from python

Table of Contents

1. What is pygetpapers
2. History
3. Formats supported by pygetpapers
4. Architecture
5. About the author and community
6. Installation
- 6.1. Method one (recommended):
- 6.2. Method two:
7. Usage
8. What is CProject?
9. Tutorial
10. Contributions
11. Feature Requests
12. Legal Implications

1. What is pygetpapers

pygetpapers is a tool to assist text miners. It makes requests to open access scientific text repositories, analyses the hits, and systematically downloads the articles without further interaction.
It comes with the packages pygetpapers and downloadtools which provide various functions to download, process and save research papers and their metadata.
The main medium of its interaction with users is through a command-line interface.
pygetpapers has a modular design which makes maintenance easy and simple. This also allows adding support for more repositories simple.

The developer documentation has been setup at readthedocs

2. History

getpapers is a tool written by Rik Smith-Unna funded by ContentMine at https://github.com/ContentMine/getpapers. The OpenVirus community requires a Python version and Ayush Garg has written an implementation from scratch, with some enhancements.

3. Formats supported by pygetpapers

pygetpapers gives fulltexts in xml and pdf format.
The metadata for papers can be saved in many formats including JSON, CSV, HTML.
Queries can be saved in form of an ini configuration file.
The additional files for papers can also be downloaded. References and citations for papers are given in XML format.
Log files can be saved in txt format.

4. Architecture

5. About the author and community

pygetpapers has been developed by Ayush Garg under the dear guidance of the OpenVirus community and Peter Murray Rust. Ayush is currently a high school student who believes that the world can only truly progress when knowledge is open and accessible by all.

Testers from OpenVirus have given a lot of useful feedback to Ayush without which this project would not have been possible.

The community has taken time to ensure that everyone can contribute to this project. So, YOU, the developer, reader and researcher can also contribute by testing, developing, and sharing.

6. Installation

Ensure that pip is installed along with python. Download python from: https://www.python.org/downloads/ and select the option Add Python to Path while installing.

Check out https://pip.pypa.io/en/stable/installing/ if difficulties installing pip.

6.1. Method one (recommended):

Ensure git cli is installed and is available in path. Check out (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
Enter the command: pip install git+git://github.com/petermr/pygetpapers
Ensure pygetpapers has been installed by reopening the terminal and typing the command pygetpapers
You should see a help message come up.

6.2. Method two:

Manually clone the repository and run python setup.py install from inside the repository directory
Ensure pygetpapers has been installed by reopening the terminal and typing the command pygetpapers
You should see a help message come up.

7. Usage

pygetpapers is a commandline tool. You can ask for help by running:

pygetpapers --help

usage: pygetpapers [-h] [--config CONFIG] [-v] [-q QUERY] [-o OUTPUT] [--save_query] [-x] [-p] [-s] [-z]
                   [--references REFERENCES] [-n] [--citations CITATIONS] [-l LOGLEVEL] [-f LOGFILE] [-k LIMIT]
                   [-r RESTART] [-u UPDATE] [--onlyquery] [-c] [--makehtml] [--synonym] [--startdate STARTDATE]
                   [--enddate ENDDATE] [--terms TERMS] [--api API] [--filter FILTER]

Welcome to Pygetpapers version 0.0.6.3. -h or --help for help

optional arguments:
  -h, --help            show this help message and exit
  --config CONFIG       config file path to read query for pygetpapers
  -v, --version         output the version number
  -q QUERY, --query QUERY
                        query string transmitted to repository API. Eg. "Artificial Intelligence" or "Plant Parts". To
                        escape special characters within the quotes, use backslash. Incase of nested quotes, ensure
                        that the initial quotes are double and the qutoes inside are single. For eg: `'(LICENSE:"cc
                        by" OR LICENSE:"cc-by") AND METHODS:"transcriptome assembly"' ` is wrong. We should instead
                        use `"(LICENSE:'cc by' OR LICENSE:'cc-by') AND METHODS:'transcriptome assembly'"`
  -o OUTPUT, --output OUTPUT
                        output directory (Default: Folder inside current working directory named )
  --save_query          saved the passed query in a config file
  -x, --xml             download fulltext XMLs if available
  -p, --pdf             download fulltext PDFs if available
  -s, --supp            download supplementary files if available
  -z, --zip             download files from ftp endpoint if available
  --references REFERENCES
                        Download references if available. Requires source for references
                        (AGR,CBA,CTX,ETH,HIR,MED,PAT,PMC,PPR).
  -n, --noexecute       report how many results match the query, but don't actually download anything
  --citations CITATIONS
                        Download citations if available. Requires source for citations
                        (AGR,CBA,CTX,ETH,HIR,MED,PAT,PMC,PPR).
  -l LOGLEVEL, --loglevel LOGLEVEL
                        Provide logging level. Example --log warning <<info,warning,debug,error,critical>>,
                        default='info'
  -f LOGFILE, --logfile LOGFILE
                        save log to specified file in output directory as well as printing to terminal
  -k LIMIT, --limit LIMIT
                        maximum number of hits (default: 100)
  -r RESTART, --restart RESTART
                        Reads the json and makes the xml files. Takes the path to the json as the input
  -u UPDATE, --update UPDATE
                        Updates the corpus by downloading new papers. Takes the path of metadata json file of the
                        orignal corpus as the input. Requires -k or --limit (If not provided, default will be used)
                        and -q or --query (must be provided) to be given. Takes the path to the json as the input.
  --onlyquery           Saves json file containing the result of the query in storage. The json file can be given to
                        --restart to download the papers later.
  -c, --makecsv         Stores the per-document metadata as csv.
  --makehtml            Stores the per-document metadata as html.
  --synonym             Results contain synonyms as well.
  --startdate STARTDATE
                        Gives papers starting from given date. Format: YYYY-MM-DD
  --enddate ENDDATE     Gives papers till given date. Format: YYYY-MM-DD
  --terms TERMS         Location of the txt file which contains terms serperated by a comma which will beOR'ed among
                        themselves and AND'ed with the query
  --api API             API to search [eupmc, crossref,arxiv,biorxiv,medrxiv,rxivist-bio,rxivist-med] (default: eupmc)
  --filter FILTER       filter by key value pair, passed straight to the crossref api only

Queries are build using -q flag. The query format can be found at http://europepmc.org/docs/EBI_Europe_PMC_Web_Service_Reference.pdf A condensed guide can be found at https://github.com/petermr/pygetpapers/wiki/query-format

8. What is CProject?

A CProject is a directory structure that the AMI toolset uses to gather and process data. Each paper gets its folder. A CTree is a subdirectory of a CProject that deals with a single paper.

9. Tutorial

pygetpapers was on version 0.0.6.4. when the tutorials were documented.

pygetpapers supports multiple APIs including eupmc, crossref,arxiv,biorxiv,medrxiv,rxivist-bio,rxivist-med. By default, it queries EPMC. You can specify the API by using --api flag.

Features	EPMC	crossref	arxiv	biorxiv	medarxiv	rxvist
Fulltext formats	xml, pdf	NA	NA	xml	xml	xml
Metdata formats	json, html, csv	json, xml, csv	json	json, csv, html	json, csv, html	json, html, csv
`--query`	yes	yes	yes	NA	NA	NA
`--update`	yes	NA	NA	yes	yes
`--restart`	yes
`--citation`	yes	NA	NA	NA	NA	NA
`--references`	yes	NA	NA	NA	NA	NA
`--terms`	yes	yes	yes	NA	NA	NA

9.1. EPMC (Default API)

9.1.1. Example Query

Let's break down the following query:

pygetpapers -q "METHOD: invasive plant species" -k 10 -o "invasive_plant_species_test" -c --makehtml -x --save_query

Flag	What it does	In this case `pygetpapers`...
`-q`	specifies the query	queries for 'essential oil' in METHODS section
`-k`	number of hits (default 100)	limits hits to 30
`-o`	specifies output directory	outputs to essential_oil_30
`-x`	downloads fulltext xml
`-c`	downloads per-paper metadata into a single csv	downloads single CSV named `europe_pmc.csv`
`--makehtml`	downloads per-paper metadata into a single HTML file	downloads single HTML named `europe_pmc.html`

pygetpapers, by default, writes metadata to a JSON file within:

individual paper directory for corresponding paper (epmc_result.json)
working directory for all downloaded papers (epmc_results.json)

OUTPUT:

INFO: Final query is METHOD: invasive plant species
INFO: Total Hits are 17910
0it [00:00, ?it/s]WARNING: Keywords not found for paper 1
WARNING: Keywords not found for paper 4
1it [00:00, 164.87it/s]
INFO: Saving XML files to C:\Users\shweata\invasive_plant_species_test\*\fulltext.xml
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:21<00:00,  2.11s/it]

9.1.2. Scope the number of hits for a query

If you are just scoping the number of hits for a given query, you can use -n flag as shown below.

pygetpapers -n -q "essential oil"

OUTPUT:

INFO: Final query is essential oil
INFO: Total number of hits for the query are 190710

9.1.3. Update an existing CProject with new papers by feeding the metadata JSON

The --update command is used to update a CProject with a new set of papers on same or different query. If let's say you have a corpus of a 30 papers on 'essential oil' (like before) and would like to download 20 more papers to the same CProject directory, you use --update command.

--update flags takes the eupmc_results.JSON's absolute path present in the CProject directory. INPUT:

pygetpapers --update "C:\Users\shweata\essential_oil_30_1\eupmc_results.JSON" -q "lantana" -k 20 -x

OUTPUT:

INFO: Final query is lantana
INFO: Total Hits are 1909
0it [00:00, ?it/s]WARNING: html url not found for paper 1
WARNING: pdf url not found for paper 1
WARNING: Keywords not found for paper 2
WARNING: Keywords not found for paper 3
WARNING: Author list not found for paper 5
WARNING: Author list not found for paper 8
WARNING: Keywords not found for paper 9
WARNING: Keywords not found for paper 11
WARNING: Keywords not found for paper 19
1it [00:00, 216.37it/s]
INFO: Saving XML files to C:\Users\shweata\essential_oil_30_1\*\fulltext.xml
100%|██████████████████████████████████████████████████████████████████████████████████| 50/50 [01:28<00:00,  1.78s/it]

9.1.3.1. How is `--update` different from just downloading x number of papers to the same output directory?

By using --update command you can be sure that there are no duplicate papers. You can't be sure when you just download x number of papers to the output directory.

9.1.4. Restart downloading papers to an existing CProject

--restart flag can be used for two purposes: -To download papers in different format. Let's say you downloaded XMLs in the first round. If you want to download pdfs for same set of papers, you use this flag.

Continue the download from the stage where it broke. This feature would particularly come in handy if you are on poor lines. You can resume downloading at whatever stage you cut off by using the update flag as we've described. --restart flag takes in the absolute path of the JSON metadata file.
```
pygetpapers --restart "C:\Users\shweata\essential_oil_30_1\eupmc_results.JSON" -q "lantana" -x -p
```

9.1.4.1. Difference between `--restart` and `--update`

If you aren't looking download new set of papers but would want to download a papers in different format for existing papers, --restart is the flag you'd want to use
If you are looking to download a new set of papers to an existing Cproject, then you'd use --update command. You should note that the format in which you download papers would only apply to the new set of papers and not for the old.

9.1.5. Downloading citations and references for papers, if available

--references and --citations flags can be used to download the references and citations respectively.
It also requires source for references (AGR,CBA,CTX,ETH,HIR,MED,PAT,PMC,PPR)

pygetpapers -q "lantana" -k 10 -o "test" -c -x --citation PMC

9.1.6. 9.1.6.Downloading only the metadata

If you are looking to download just the metadata in the supported formats--onlyquery is the flag you use. It saves the metadata in the output directory.

You can use --restart feature to download the fulltexts for these papers. INPUT:

pygetpapers --onlyquery -q "lantana" -k 10 -o "lantana_test" -c

OUTPUT:

INFO: Final query is lantana
INFO: Total Hits are 1909
0it [00:00, ?it/s]WARNING: html url not found for paper 1
WARNING: pdf url not found for paper 1
WARNING: Keywords not found for paper 2
WARNING: Keywords not found for paper 3
WARNING: Author list not found for paper 5
WARNING: Author list not found for paper 8
WARNING: Keywords not found for paper 9
1it [00:00, 407.69it/s]

9.1.7. Download papers within certain start and end date range

By using --startdate and --enddate you can specify the date range within which the papers you want to download were first published.

pygetpapers -q "METHOD:essential oil" --startdate "2020-01-02" --enddate "2021-09-09"

9.1.8. Saving query for later use

To save a query for later use, you can use --save_query. What it does is that it saves the query in a .ini file in the output directory.

pygetpapers -q "lantana" -k 10 -o "lantana_query_config"--save_query

Here is an example config file pygetpapers outputs

9.1.9. Feed query using `config.ini` file

Using can use the config.ini file you created using --save_query, you re-run the query. To do so, you will give --config flag the absolute path of the saved_config.ini file.

pygetpapers --config "C:\Users\shweata\lantana_query_config\saved_config.ini"

9.1.10. Querying using a term list

If your query is complex with multiple ORs, you can use --terms feature. To use this, you will:

Create a .txt file with list of terms separated by commas.
Give the --terms flag the absolute path of the .txt file

-q is optional.The terms would be OR'ed with each other ANDed with the query, if given.

INPUT:

pygetpapers -q "essential oil" --terms C:\Users\shweata\essential_oil_terms.txt -k 10 -o "terms_test_essential_oil" -x

OUTPUT:

C:\Users\shweata>pygetpapers -q "essential oil" --terms C:\Users\shweata\essential_oil_terms.txt -k 10 -o "terms_test_essential_oil"
INFO: Final query is (essential oil AND (antioxidant OR  antibacterial OR  antifungal OR  antiseptic OR  antitrichomonal agent))
INFO: Total Hits are 43397
0it [00:00, ?it/s]WARNING: Author list not found for paper 9
1it [00:00, 1064.00it/s]
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:19<00:00,  1.99s/it]

You can also use this feature to download papers by using the PMC Ids. You can feed the .txt file with PMC ids comman-separated. Make sure to give a large enough hit number to download all the papers specified in the text file.

Example text file can be found, here INPUT:

pygetpapers --terms C:\Users\shweata\PMCID_pygetpapers_text.txt -k 100 -o "PMCID_test"

OUTPUT:

INFO: Final query is (PMC6856665 OR  PMC6877543 OR  PMC6927906 OR  PMC7008714 OR  PMC7040181 OR  PMC7080866 OR  PMC7082878 OR  PMC7096589 OR  PMC7111464 OR  PMC7142259 OR  PMC7158757 OR  PMC7174509 OR  PMC7193700 OR  PMC7198785 OR  PMC7201129 OR  PMC7203781 OR  PMC7206980 OR  PMC7214627 OR  PMC7214803 OR  PMC7220991
)
INFO: Total Hits are 20
WARNING: Could not find more papers
1it [00:00, 505.46it/s]
100%|█████████████████████████████████████████████| 20/20 [00:32<00:00,  1.61s/it]

9.1.11. 9.1.11 Log levels

You can specify the log level using the -l flag. The default as you've already seen so far is info.

INPUT:

pygetpapers -q "lantana" -k 10 -o lantana_test_10_2 --loglevel debug -x

9.1.12. Log file

You can also choose to write the log to a .txt file while simultaneously printing it out.

INPUT:

pygetpapers -q "lantana" -k 10 -o lantana_test_10_4 --loglevel debug -x --logfile test_log.txt

9.2. Crossref

You can query crossref api only for the metadata.

9.2.1. Sample query

The metadata formats flags are applicable as described in the EPMC tutorial
--terms and -q are also applicable to crossref INPUT:

pygetpapers --api crossref -q "essential oil" --terms C:\Users\shweata\essential_oil_terms.txt -k 10 -o "terms_test_essential_oil_crossref_3" -x -c --makehtml

OUTPUT:

INFO: Final query is (essential oil AND (antioxidant OR  antibacterial OR  antifungal OR  antiseptic OR  antitrichomonal agent))
INFO: Making request to crossref
INFO: Got request result from crossref
INFO: Making csv files for metadata at C:\Users\shweata\terms_test_essential_oil_crossref_3
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 185.52it/s]
INFO: Making html files for metadata at C:\Users\shweata\terms_test_essential_oil_crossref_3
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 87.98it/s]
INFO: Making xml files for metadata at C:\Users\shweata\terms_test_essential_oil_crossref_3
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 366.97it/s]
INFO: Wrote metadata file for the query
INFO: Writing metadata file for the papers at C:\Users\shweata\terms_test_essential_oil_crossref_3
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 996.82it/s]

9.2.2. Filter

9.3. arxiv

pygetpapers allows you to query arxiv wrapper for metadata and get results in XML format.

9.3.1. Sample query

INPUT

pygetpapers --api arxiv -k 10 -o arxiv_test_2 -q "artificial intelligence" -x

OUTPUT


INFO: Final query is artificial intelligence
INFO: Making request to Arxiv through pygetpapers
INFO: Got request result from Arxiv through pygetpapers
INFO: Requesting 10 results at offset 0
INFO: Requesting page of results
INFO: Got first page; 10 of 10 results available
INFO: Making xml files for metadata at C:\Users\shweata\arxiv_test_2
100%|█████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 427.09it/s]
100%|█████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 982.89it/s]

9.4. Biorxiv and Medrxiv

You can query biorxiv and medrxiv for fulltext and metadata (in all available formats)

9.4.1. Sample Query

INPUT:

pygetpapers --api biorxiv --startdate 2021-04-01 -o biorxiv_test -x -c --makehtml  -k 20

OUTPUT:

INFO: Final query is (Default Pygetpapers Query) AND (FIRST_PDATE:[2021-04-01 TO 2021-07-19])
INFO: Making Request to rxiv
INFO: Making csv files for metadata at C:\Users\shweata\biorxiv_test
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17/17 [00:00<00:00, 253.38it/s]
INFO: Making html files for metadata at C:\Users\shweata\biorxiv_test
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17/17 [00:00<00:00, 218.29it/s]
INFO: Making xml for paper
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17/17 [00:33<00:00,  1.99s/it]
INFO: Wrote metadata file for the query
INFO: Writing metadata file for the papers at C:\Users\shweata\biorxiv_test
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 17/17 [00:00<00:00, 1369.32it/s]

9.4.2. `--update`

Ensure that you specify the --api you used to download the existing corpus while updating. INPUT:

pygetpapers --api biorxiv --update C:\Users\shweata\biorxiv_test_4\rxiv-results.json -k 10 --startdate 2021-07-03

OUTPUT:

INFO: Final query is (False) AND (FIRST_PDATE:[2021-07-03 TO 2021-07-21])
INFO: Reading old json metadata file
INFO: Making Request to rxiv
INFO: Wrote metadata file for the query
INFO: Writing metadata file for the papers at C:\Users\shweata

9.5.1. Sample Query

INPUT

pygetpapers --api medrxiv --startdate 2021-04-01 -o medrxiv_test_2 -x -c -p  --makehtml -k 20

OUTPUT

INFO: Final query is (Default Pygetpapers Query) AND (FIRST_PDATE:[2021-04-01 TO 2021-07-19])
INFO: Making Request to rxiv
INFO: Making csv files for metadata at C:\Users\shweata\medrxiv_test_2
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 168.70it/s]
INFO: Making html files for metadata at C:\Users\shweata\medrxiv_test_2
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 229.12it/s]
INFO: Making xml for paper
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:38<00:00,  1.92s/it]
INFO: Wrote metadata file for the query
INFO: Writing metadata file for the papers at C:\Users\shweata\medrxiv_test_2
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 20/20 [00:00<00:00, 241.71it/s]

--update would work the same as medarxiv

9.6. rxivist

Queries both biorxiv and medarxiv. The difference here is that you can specify a query. But rxivist has now clubbed biorxiv and medarxiv. That would mean that your downloads would be a mixture of both.

You can only retrieve metadata from rxivist.

INPUT:

pygetpapers --api rxivist -q "biomedicine" -k 10 -c -x -o "biomedicine_rxivist" --makehtml -p

OUTPUT:

WARNING: Pdf is not supported for this api
INFO: Final query is biomedicine
INFO: Making Request to rxivist
INFO: Making csv files for metadata at C:\Users\shweata\biomedicine_rxivist
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 125.54it/s]
INFO: Making html files for metadata at C:\Users\shweata\biomedicine_rxivist
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 124.71it/s]
INFO: Making xml files for metadata at C:\Users\shweata\biomedicine_rxivist
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 633.38it/s]
INFO: Wrote metadata file for the query
INFO: Writing metadata file for the papers at C:\Users\shweata\biomedicine_rxivist
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:00<00:00, 751.09it/s]

10. Contributions

Contributions are welcome through issues as well as pull requests. For direct contributions, you can mail the author at [email protected].

To discuss problems or feature requests, file an issue. For bugs, please include as much information as possible, including operating system, python version, and version of all dependencies.

To contribute, make a pull request. Contributions should include tests for any new features/bug fixes and follow best practices including PEP8, etc.

11. Feature Requests

To request features, please put them in issues

12. Legal Implications

If you usepygetpapers, you should be careful to understand the law as it applies to their content mining, as they assume full responsibility for their actions when using the software.

12.1. Countries with copyright exceptions for content mining:

UK
Japan

12.2. Countries with proposed copyright exceptions:

Ireland
EU countries

12.3. Countries with permissive interpretations of 'fair use' that might allow content mining:

Israel
USA
Canada

12.4. General summaries and guides:

"The legal framework of text and data mining (TDM)", carried out for the European Commission in March 2014 (PDF)
"Standardisation in the area of innovation and technological development, notably in the field of Text and Data Mining", carried out for the European Commission in 2014 (PDF)

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docs		docs
pygetpapers		pygetpapers
resources		resources
tests		tests
.gitattributes		.gitattributes
.gitignore		.gitignore
LICENSE		LICENSE
MANIFEST.in		MANIFEST.in
README.md		README.md
init.py		init.py
requirements.txt		requirements.txt
setup.py		setup.py

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Research Papers right from python

1. What is pygetpapers

2. History

3. Formats supported by pygetpapers

4. Architecture

5. About the author and community

6. Installation

6.1. Method one (recommended):

6.2. Method two:

7. Usage

8. What is CProject?

9. Tutorial

9.1. EPMC (Default API)

9.1.1. Example Query

9.1.2. Scope the number of hits for a query

9.1.3. Update an existing CProject with new papers by feeding the metadata JSON

9.1.3.1. How is --update different from just downloading x number of papers to the same output directory?

9.1.4. Restart downloading papers to an existing CProject

9.1.4.1. Difference between --restart and --update

9.1.5. Downloading citations and references for papers, if available

9.1.6. 9.1.6.Downloading only the metadata

9.1.7. Download papers within certain start and end date range

9.1.8. Saving query for later use

9.1.9. Feed query using config.ini file

9.1.10. Querying using a term list

9.1.11. 9.1.11 Log levels

9.1.12. Log file

9.2. Crossref

9.2.1. Sample query

9.2.2. Filter

9.3. arxiv

9.3.1. Sample query

9.4. Biorxiv and Medrxiv

9.4.1. Sample Query

9.4.2. --update

9.5.1. Sample Query

9.6. rxivist

10. Contributions

11. Feature Requests

12. Legal Implications

12.1. Countries with copyright exceptions for content mining:

12.2. Countries with proposed copyright exceptions:

12.3. Countries with permissive interpretations of 'fair use' that might allow content mining:

12.4. General summaries and guides:

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9.1.3.1. How is `--update` different from just downloading x number of papers to the same output directory?

9.1.4.1. Difference between `--restart` and `--update`

9.1.9. Feed query using `config.ini` file

9.4.2. `--update`

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