BatLit Reference List

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 in many ways, including, but not limited to, external storage media, Zenodo, and GitHub. 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).

by Aja C. Sherman (curator, batbase.org), Jorrit H. Poelen (reviewer, archivist), Donat Agosti (reviewer, Plazi), Nathan Upham (reviewer, mammaldiversity.org), Cullen K. Geiselman (reviewer, batbase.org).

Cite as:

Sherman, A.C., ...[add more names here], Simmons, N.B., Zijlstra, J.S., Geiselman C.K. 2024. Bat Literature Project (BatLit, https://batlit.org) v0.7 hash://md5/ce1e7618f237ff56e74d51f496e811a3 .

with contributions from DeeAnn Reeder, Nancy Simmons, Kendra Phelps, ...

⚠️ 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

One way BatLit can be searched and discovered is 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

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 various channels such as local storage media (e.g., external harddisk), GitHub pages and Zenodo.

(Bat Literature Zotero Group) -[:track]-> (Bat Literature Corpus) 

(Bat Literature Corpus) -[:publish]-> (https://bat-literature.github.io)

(Bat Literature Corpus) -[:publish]-> (Zenodo BLR)

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

1. BatLit community solicits bat literature references and their associated digital copies
2. provided literature references and digital copies (e.g., pdfs) are reviewed
3. on passing review, literature references are added to BatLit

Feedback Workflow

1. BatLit Community Solicits feedback on published BatLit versions
2. on receiving feedback, the batlit curator documents the request in a github issue at https://github.com/bat-literature/bat-literature.github.io/issues .
3. open issues are reviewed by the editorial board under guidance of the curator
4. if needed, existing records are updated to address the provided issue

Deduplication Workflow

1. Data curator merges duplicate entries entries using the Zotero merge tool
2. Data archivist take a versioned snapshot of the Zotero group
3. 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

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

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.

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 again 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.

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
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
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
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

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