bat-literature
BatLit: The Bat Literature Project
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BatLit Search
There’s many ways to search in BatLit. One way is to go to the BatLit References page and use ctlr-f to find a citation. Another way is to use a more advanced search made available through the Zenodo API, with some simple examples shown below.
Example Searches
Works published in 1994 mentioning “Koopman”:
Plazi’s Literature Search Prototype, which uses the same Zenodo API and technologies (e.g., html/javascript) in a more sophisticated way, can be found below:
Introduction
Bat researchers rely on access to a vast corpus of bat literature to help advance our understanding of bats and the ecosystems they live in. Many researchers build and organize their personal literature collections using mainstream digital tools like Zotero and EndNote, whereas others use homegrown digital methods or even manage their collections manually. However, all researchers routinely encounter roadblocks to literature access including paywalls and older literature resources that have not yet been digitized. To help provide access to bat research literature for all, Plazi and the GBatNet Bat Eco-Interactions Working Group are compiling the Bat Literature Corpus (BatLit). BatLit is an actively managed, digital, versioned, and citable collection of bat research literature and associated metadata compiled from existing literature contributed by bat researchers. BatLit is designed to be used in manual (e.g., point-and-click) as well as automated workflows (e.g., text mining, language model training), and can be accessed through Zenodo. As BatLit continues to improve and grow, we aim to continue to democratize access to bat literature, accelerate research, and help reduce the barrier to knowledge for bat researchers around the world. We invite you to contribute your reference library, especially the PDFs, to BatLit and thereby help increase information access for all.
The Bat Literature Project (BatLit) facilitates discovery of scientific literature on bats (Chiroptera).
For more information contact Aja Sherman (aja.sherman22@gmail.com), Cullen Geiselman (cullen@werinterests.com), or Jorrit Poelen (jhpoelen@jhpoelen.nl).
Cite as: A.C. Sherman, J.H. Poelen, D. Agosti, N. Upham, N.B. Simmons, J.S. Zijlstra, and C.K. Geiselman. 2024. Bat Literature Project (BatLit, https://batlit.org) v0.7 hash://md5/ce1e7618f237ff56e74d51f496e811a3 https://doi.org/10.5281/zenodo.14662695 .
⚠️ this is a work in progress⚠️
Getting Started
If you’d like to explore BatLit, please review the examples below. Alternatively, if you’d like to learn more about why BatLit exists, and how it was built, please skip to the Introduction.
Searching for Literature by Keywords
BatLit can be searched and discovered through Zenodo at https://zenodo.org/communities/batlit. Zenodo offers search features through a point-and-click web interface, as well as a Web Application Programming Interface (Web API, https://developers.zenodo.org).
For instance, let’s say that Carla would like to search for literature that mention “Rhinolophus sinicus” in their associated metadata (e.g., title, abstract). She uses Zenodo and enters “Rhinolophus sinicus” in the search box of the BatLit community producing the following query: https://zenodo.org/communities/batlit/records?q=rhinolophus%20sinicus . On inspecting the initial results, she limits to see only publications that are openly available by selecting Access Status > Open in the Zenodo web search results.
Searching by Zotero Record Identifiers
BatLit is managed in Zotero. Each Zotero record has a group id and an item id. These ids uniquely identify a record. These ids are combined to create a life science identifier for each Zotero literature record with the following syntax:
urn:lsid:zotero.org:groups:[group id]:items:[item id]
For example, the Zotero record with group id 5435545 (the batlit group) and item id C4GD9Y6Q has a lsid:
urn:lsid:zotero.org:groups:5435545:items:C4GD9Y6Q
Now, you can search Zenodo for deposits (publications) related to this particular Zotero record by putting the lsid (in double quotes) in the search box. After hitting “enter”, you are directed to the following search results page .
The example above shows that BatLit records in Zotero are linked to their derived records in Zenodo by their record identifiers.
More Advanced Queries
Because BatLit is integrated with Zenodo, you can benefit from the powerful features of the Zenodo Web Search and Zenodo Web API for discovery. See https://developers.zenodo.org for more information.
Contributing
If you have any comments, suggestions, or questions, please open an issue.
Version History
| name | version | date | size | # pages | # references | # attachments | fingerprint |
|---|---|---|---|---|---|---|---|
| Bat Literature Corpus | v0.1 | 2024-04-26 | 7.9 GiB | 2929 | 5055 | hash://sha256/6ba…189 | |
| Bat Literature Corpus | v0.2 | 2024-05-16/2024-05-17 | 11.6 GiB | 3310 | 5471 | hash://md5/be6…1d7 | |
| Bat Literature Corpus | v0.3 | 2024-06-25/2024-06-26 | 13.6 GiB | 5501 | 7229 | hash://md5/350…77d | |
| Bat Literature Corpus | v0.4 | 2024-08-01/2024-08-02 | 50.9 GiB | 20146 | 29860 | hash://md5/b39…72a | |
| Bat Literature Corpus | v0.5 | 2024-08-16/2024-08-17 | 50.9 GiB | 20145 | 29850 | hash://md5/26f…b20 | |
| Bat Literature Corpus | v0.6 | 2024-09-19/2024-09-20 | 44.7GiB | 427105 | 19038 | 22590 | hash://md5/db7…97b |
| Bat Literature Corpus | v0.7 | 2024-12-05/2024-12-06 | 45.2GiB | 431870 | 19268 | 22930 | hash://md5/ce1…1a3 |
Methods
We use Zotero for managing our literature corpus, and Preston for tracking their associated content in a versioned corpus. This versioned corpus is designed to be published through Zenodo.
The above figure shows how Zotero is used for managing a collection of literature references (pdfs and metadata). Versioned snapshots of this collection are securely packaged as a BatLit version. This version is then mobilized through the Zenodo BatLit community.
Curation Workflow
To help keep BatLit current (e.g., add new references) and accurate (e.g., update existing records), we’ve implemented the following curation workflows:
New References Workflow
- BatLit community solicits bat literature references and their associated digital copies
- provided literature references and digital copies (e.g., pdfs) are reviewed
- on passing review, literature references are added to BatLit Zotero community by the BatLit curator
Feedback Workflow
- BatLit Community Solicits feedback on published BatLit versions
- on receiving feedback, the batlit curator documents the request in a github issue at https://github.com/bat-literature/bat-literature.github.io/issues .
- open issues are reviewed by the editorial board under guidance of the curator
- if needed, existing records are updated to address the provided issue
Deduplication Workflow
- Data curator merges duplicate entries entries using the Zotero merge tool
- Data archivist take a versioned snapshot of the Zotero group
- Preston (or some other robot) detects relations like:
{
"...": "...",
"key": "YWNCWPYJ",
"...": "...",
"relations": {
"dc:replaces": "http://zotero.org/groups/5435545/items/2PWXAVQL"
}
"...": "...",
}
and translates this into an action to annotate any existing Zenodo record associated with http://zotero.org/groups/5435545/items/2PWXAVQL (or urn:lsid:zotero.org:groups:5435545:items:2PWXAVQL) as deprecated and being replaced by https://www.zotero.org/groups/5435545/items/YWNCWPYJ (or urn:lsid:zotero.org:groups:5435545:items:YWNCWPYJ), or
(urn:lsid:zotero.org:groups:5435545:items:2PWXAVQL)
-[:replaced_by]->
(urn:lsid:zotero.org:groups:5435545:items:YWNCWPYJ)
For context see notes related to approach curating duplicate literature entries.
Prerequisites
In the following sections, some examples are listed that uses a notation commonly used in the Unix shell, also known as the “commandline” or “terminal”. And, at the time of writing, these examples can be executed/run provided the following programs are available: preston, jq, mlr as well as more commonly available unix/posix/linux programs like grep, sort, and uniq.
To run these programs, please use some Linux distribution, MacOS, or Windows Subsystem for Linux (WSL) available on Windows 10 and higher.
Also, please make sure to install preston, jq, and mlr.
The tools used in the example workflows are designed to handle lots of data quickly using so-called “Standard Streams”. In addition, they have the ability to run offline after an initial caching (or cloning) of remote resources. If you are unfamiliar with these tools or processing methods and would like to learn more, you may benefit from a Carpentries Lesson like https://librarycarpentry.org/lc-shell/ or many of the other educational materials. Note that some of these tools have been around since the 1970s, are well documented and are likely to stick around a little while longer.
Tracking Zotero
To track the Zotero group and compile a version of the bat literature corpus, the following command is used (in bash/linux):
ZOTERO_TOKEN=[SECRET] preston track --algo md5 https://www.zotero.org/groups/5435545/bat_literature_project
Note that this group has access restrictions for copyright reasons. This is why you need to replace the “[SECRET]” with your personal access token.
Publishing Metadata
To publish the batlit metadata only (not pdfs), use the following commands
# first copy provenance index
preston cp --algo md5 --type provindex [target dir]/data
# then copy the provenance
preston cp --algo md5 --type prov [target dir]/data
cd [target dir]
# and get the associated zotero metadata
preston ls --algo md5\
| grep -v "file/view"\
| grep hasVersion\
| preston cat --algo md5 --remote file://[source dir]/data\
> /dev/null
Depositing To Zenodo
BatLit content and metadata is made available through Zenodo to facilitate access.
The following workflow can be used to deposit versioned BatLit records into Zenodo: (a) generate Zenodo compatible metadata (b) submit metadata along with their associated pdf using the Zenodo Web API.
In (a), we convert the tracked Zotero metadata into the Zenodo metadata using [preston zotero-stream]:
preston cat $(preston head --algo md5)\
| preston zotero-stream\
--anchor $(preston head --algo md5)\
--algo md5\
--communities batlit,biosyslit\
> zenodo.json
where zenodo.json contains a Zenodo metadata record on each line using the https://jsonlines.org/ format.
An example a single line from such metadata generated from a versioned BatLit corpus, in this case BatLit v0.5 hash://md5/26f7ce5dd404e33c6570edd4ba250d20, is shown below.
{
"metadata": {
"filename": "Campbell et al. - 2010 - Divergent Microclimates in Artificial and Natural .pdf",
"related_identifiers": [
{
"relation": "isAlternateIdentifier",
"identifier": "hash://md5/0ed912a0ce156ab17810d732e2b4d13d"
},
{
"relation": "isAlternateIdentifier",
"identifier": "urn:lsid:zotero.org:groups:5435545:items:IJI9WGI5"
},
{
"relation": "hasVersion",
"identifier": "hash://md5/0ed912a0ce156ab17810d732e2b4d13d"
},
{
"relation": "hasVersion",
"identifier": "hash://sha256/6b55ec617db5023a663d31dbd016f609398bf5a45991b544f240d6fb84d93779"
},
{
"relation": "isDerivedFrom",
"identifier": "zotero://select/groups/5435545/items/IJI9WGI5"
},
{
"relation": "isDerivedFrom",
"identifier": "https://zotero.org/groups/5435545/items/IJI9WGI5"
},
{
"relation": "isDerivedFrom",
"identifier": "https://linker.bio/cut:hash://md5/2717614e0b13ca488fb57c2ee6c64f2e!/b147656-150219"
},
{
"relation": "isPartOf",
"identifier": "hash://md5/26f7ce5dd404e33c6570edd4ba250d20"
},
{
"relation": "isAlternateIdentifier",
"identifier": "10.3161/150811010X504671"
},
{
"relation": "isCompiledBy",
"identifier": "10.5281/zenodo.1410543",
"resource_type": "software"
}
],
"communities": [
{
"identifier": "batlit"
},
{
"identifier": "biosyslit"
}
],
"http://www.w3.org/ns/prov#wasDerivedFrom": "https://linker.bio/cut:hash://md5/2717614e0b13ca488fb57c2ee6c64f2e!/b147656-150219",
"upload_type": "publication",
"http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "application/json",
"referenceId": "https://api.zotero.org/groups/5435545/items/IJI9WGI5",
"creators": [
{
"name": "Campbell, Susan"
},
{
"name": "Coulson, Graeme"
},
{
"name": "Lumsden, Linda F."
}
],
"publication_type": "article",
"access_right": "restricted",
"publication_date": "2010",
"title": "Divergent microclimates in artificial and natural roosts of the large-footed myotis (Myotis macropus)",
"journal_title": "Acta Chiropterologica",
"journal_volume": "12",
"journal_issue": "1",
"journal_pages": "173-185",
"keywords": [
"Biodiversity",
"Mammalia",
"Chiroptera",
"Chordata",
"Animalia",
"bats",
"bat"
],
"custom": {
"dwc:kingdom": [
"Animalia"
],
"dwc:phylum": [
"Chordata"
],
"dwc:class": [
"Mammalia"
],
"dwc:order": [
"Chiroptera"
]
},
"description": "(Uploaded by Plazi for the Bat Literature Project) The thermal environment of day roosts is considered one of the most influential factors affecting the survival, growth and reproduction of microbats. The use of torpor is a common energy saving strategy employed by microbats in temperate regions. The efficiency of entry into, and arousal from, torpor is governed by roost microclimate, primarily roost temperature. The large-footed myotis Myotis macropus roosts in both tree cavities and a man-made tunnel at Yan Yean reservoir in Victoria, Australia. We investigated the thermal properties of both roost types in comparison to available tree cavities and ambient temperature over four time periods from October 2003 to May 2005. Tree cavities and tunnel roosts remained significantly warmer at night, cooler during the day, and were more stable than ambient temperatures. In addition, roost tree cavities were significantly cooler between 10:00–13:00 h compared to available tree cavities, and there was a trend for roost tree cavities to be slightly warmer at night and slower to reach maximum temperature relative to available tree cavities during the breeding season (October–January). In contrast, there was little difference in roost and available tree cavity temperatures outside of the breeding season (April–May). Temperatures inside tunnel roosts were more stable and were significantly cooler during the afternoon compared to roost tree cavities during both the breeding and non-breeding seasons. Myotis macropus may actively trade-off the enhanced thermoregulatory benefits of warm roosts for reduced predation risk associated with the tunnel roosting environment."
}
}
Now, after generating the metadata, in (b), we deposit the records into the desired Zenodo community after tracking their version:
cat zenodo.json\
| preston track --algo md5\
| ZENODO_TOKEN=[SECRET] preston zenodo --algo md5 --communities batlit,biosyslit\
1> transfer.nq\
2> transfer.err
where transfer.nq captures the responses from Zenodo following the submission of the records, and transfer.err contains the error logs related to the submission of the record.
Please refer to –help pages for [preston zenodo] for more information on ways to update metadata, force new versions etc.
:warning: please use the https://sandbox.zenodo.org to test record submission workflows before using the production endpoint at https://zenodo.org . :warning:
Verifying Access to BatLit Content
The internet is a dynamic place, and content gets destroyed, damaged, lost, or misplaced, even in large, trusted infrastructures.
In order to verify whether BatLit content is available on Zenodo (or elsewhere), the following procedure can be used to check whether BatLit associated content can be found, accessed, integrated, and reused:
export ZENODO_TOKEN=[SECRET]
# ^^^^
# needed only to access restricted content
preston verify\
--algo md5\
--remote https://batlit.org/data,https://zenodo.org\
--anchor hash://md5/db73e659e8cf16ef50e82bb5e72ae97b
where
preston verify
is the command that goes through the inventory of BatLit Corpus, and attempts to retrieve content from https://batlit.org first (metadata), then from Zenodo (pdfs) unless the content is already available locally.
Note that
--anchor hash://md5/db73e659e8cf16ef50e82bb5e72ae97b
specifies the fingerprint of the version you’d like to verify. In this case the fingerprint refers to BatLit Corpus v0.6 .
In other words, a method exists to help periodically verify that BatLit related content is accessible. The workflow shown above is the equivalent of clicking on all the ~20k download buttons in the BatLit associated Zenodo html pages in addition to checking each and every entry in BatLit Corpus for a corresponding content.
Note on BatLit content in Zenodo
Note that after submission of Zenodo-compatible (at least at time of writing) metadata generated from a specific batlit version, Zenodo software or community editors, may choose to reformat, or otherwise change, the metadata associated with a submitted record at some point in the future. Due to Zenodo’s design, record metadata is not version controlled and may change in the future and deviate from their original, immutable, BatLit version. In other words, BatLit associated content on Zenodo should be considered as a possibly incomplete or changed copy of the content associated with an original BatLit version. This is why it is recommended to use (or at least cite) the original batlit corpus when using the corpus for research purposes or automated workflows.
Statistics
Estimating number of references in a corpus version -
preston cat --remote https://linker.bio hash://md5/ce1e7618f237ff56e74d51f496e811a3\
| grep "items[?]"\
| grep hasVersion\
| preston cat --remote https://linker.bio\
| jq -c '.[]'\
| jq --raw-output -c '.data | select(has("creators"))'\
| wc -l
Estimating number of associated corpus pdfs -
preston cat --remote https://linker.bio hash://md5/ce1e7618f237ff56e74d51f496e811a3\
| grep "file/view"\
| grep hasVersion\
| grep hash\
| wc -l
Estimating the total volume of data for the most recent (i.e. “head”) version
preston cat --remote https://linker.bio hash://md5/ce1e7618f237ff56e74d51f496e811a3\
| grep hasVersion\
| grep -oE "hash://md5/[a-f0-9]{32}"\
| sort\
| uniq\
| preston cat\
| pv > /dev/null
Results
Example of Tracked Zotero Record
An example of a tracked Zotero record generated using
preston cat --remote https://linker.bio hash://md5/ce1e7618f237ff56e74d51f496e811a3\
| grep "items[?]"\
| grep hasVersion\
| preston cat --remote https://linker.bio\
| jq -c '.[]'\
| head -n1\
| jq .
is shown below:
{
"key": "376ZATI8",
"version": 62023,
"library": {
"type": "group",
"id": 5435545,
"name": "Bat Literature Project",
"links": {
"alternate": {
"href": "https://www.zotero.org/groups/bat_literature_project",
"type": "text/html"
}
}
},
"links": {
"self": {
"href": "https://api.zotero.org/groups/5435545/items/376ZATI8",
"type": "application/json"
},
"alternate": {
"href": "https://www.zotero.org/groups/bat_literature_project/items/376ZATI8",
"type": "text/html"
},
"attachment": {
"href": "https://api.zotero.org/groups/5435545/items/5PUDTPS6",
"type": "application/json",
"attachmentType": "application/pdf",
"attachmentSize": 1407714
}
},
"meta": {
"createdByUser": {
"id": 13229919,
"username": "acsherman",
"name": "",
"links": {
"alternate": {
"href": "https://www.zotero.org/acsherman",
"type": "text/html"
}
}
},
"creatorSummary": "Guillen-Servent et al.",
"parsedDate": "2003",
"numChildren": 1
},
"data": {
"key": "376ZATI8",
"version": 62023,
"itemType": "bookSection",
"title": "Phylogeography and biogeography of the horseshoe bats (Chiroptera: Rhinolophidae)",
"creators": [
{
"creatorType": "author",
"firstName": "A.",
"lastName": "Guillen-Servent"
},
{
"creatorType": "author",
"firstName": "C. M.",
"lastName": "Francis"
},
{
"creatorType": "author",
"firstName": "",
"lastName": "Ricklefs, Robert E."
}
],
"abstractNote": "",
"bookTitle": "Horseshoe bats of the World (Chiroptera: Rhinolophidae) Shropshire",
"series": "",
"seriesNumber": "",
"volume": "",
"numberOfVolumes": "",
"edition": "",
"place": "Shropshire",
"publisher": "Alana Books",
"date": "2003",
"pages": "",
"language": "",
"ISBN": "",
"shortTitle": "",
"url": "",
"accessDate": "",
"archive": "",
"archiveLocation": "",
"libraryCatalog": "",
"callNumber": "",
"rights": "",
"extra": "",
"tags": [],
"collections": [
"UAWY6DNP"
],
"relations": {},
"dateAdded": "2024-12-05T16:49:47Z",
"dateModified": "2024-12-05T16:52:11Z"
}
}
Literature Records by Type
The tracked metadata was used to list the kinds of content included in the Bat Literature Corpus.
The follow bash script was used to generated the content type frequency table below.
cat\
<(echo count contentType)\
<(preston cat --remote https://linker.bio hash://md5/ce1e7618f237ff56e74d51f496e811a3 | grep items? | grep hasVersion | preston cat --remote https://linker.bio | jq --raw-output '.[].data.itemType' | sort | uniq -c | sort -nr)\
| mlr --ipprint --omd cat
Note that there’s roughly two kinds of content: top level content like journal articles, books, reports and conference papers. These top level content may have one of more association with associated content like attachments, notes, and annotations. These types are provided by Zotero. You can find background on these contentTypes (aka item types) at https://www.zotero.org/support/kb/item_types_and_fields .
| count | contentType |
|---|---|
| 24175 | attachment |
| 18373 | journalArticle |
| 637 | note |
| 360 | book |
| 282 | bookSection |
| 99 | report |
| 95 | annotation |
| 54 | thesis |
| 34 | conferencePaper |
| 28 | preprint |
| 15 | dataset |
| 14 | magazineArticle |
| 6 | webpage |
| 2 | newspaperArticle |
| 1 | presentation |
Literature Record Index
Literature records can be extracted from this corpus in various ways. As an example, we show the output of an executed script in bin/list-refs.sh against a recent version of the BatLit Corpus. For ease of processing, we’ve included a sample of 3 records in the table below, as well as files in tsv/csv formats include 100 records and all records.
| filenames | description |
|---|---|
| refs-100.tsv / refs-100.csv | author/date/title/journal of first 100 records |
| refs.tsv / refs.csv | author/date/title/journal of all records |
First 3 records shown below as an example. This data is also used to create the BatLit References Page. This page adds links to the references to facilitate searches on Zenodo.
Note that id points to the records as seen on Zotero, attachment points to the attachment records as seen on Zotero, attachmentId is the signature/hash of the associated pdf, corpusId is the signature/hash of the applicable BatLit version.
authors Douglas
date 1967
title Article: The Natural History of the Ghost Bat, Macroderma Gigas (Microchiroptera Megadermatidae), in Western Australia
journal Western Australia. The Western Australian Naturalist
type journalArticle
volume 10
issue
pages 125-138
doi
id https://www.zotero.org/groups/bat_literature_project/items/M5MZ6NSB
attachment https://api.zotero.org/groups/5435545/items/223GU789
attachmentId hash://md5/5e3f7fac483550be7983c6096e9e9800
corpusId hash://md5/ce1e7618f237ff56e74d51f496e811a3
authors Vora | Hannah | Lieberman | Vale | Plowright | Bernstein
date 2022-05
title Want to prevent pandemics? Stop spillovers
journal Nature
type journalArticle
volume 605
issue 7910
pages 419-422
doi 10.1038/d41586-022-01312-y
id https://www.zotero.org/groups/bat_literature_project/items/A5RNP5YH
attachment https://api.zotero.org/groups/5435545/items/223P42N5
attachmentId hash://md5/85c89cedcc23b072f98f3c22ad731029
corpusId hash://md5/ce1e7618f237ff56e74d51f496e811a3
authors Otto | Rall | Brose
date 12/2007
title Allometric degree distributions facilitate food-web stability
journal Nature
type journalArticle
volume 450
issue 7173
pages 1226-1229
doi 10.1038/nature06359
id https://www.zotero.org/groups/bat_literature_project/items/6RAB386Y
attachment https://api.zotero.org/groups/5435545/items/225DJR2Q
attachmentId hash://md5/6bdc818006c01cac3dd90eec4b337289
corpusId hash://md5/ce1e7618f237ff56e74d51f496e811a3