Mapping between IPNI names and bibliographic identifiers
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README.md

ipni-names

Mapping between names in the International Plant Names Index IPNI names and bibliographic identifiers.

Names and publications are mapped to a series of bibliographic identifiers, including DOIs, article identifiers from BioStor, JSTOR, and CiNii, Handles, URLs, and PDFs. Individual pages may also be mapped to BHL PageIDs.

This repository stores the current mapping for a subset of the journals in IPNI, these are in the journals folder as csv (comma separated value) files. For example, the mapping for the Edinburgh Journal of Botany ISSN 0960-4286 is in the file edinburgh j. bot..csv. This journal has had every name mapped to a DOI, for example

77104049-1 Begonia rubiteae was published in article DOI:10.1017/S0960428609990266

Hughes, M., Coyle, C., & Rubite, R. R. (2010, March). A REVISION OF BEGONIA SECTION DIPLOCLINIUM (BEGONIACEAE) ON THE PHILIPPINE ISLAND OF PALAWAN, INCLUDING FIVE NEW SPECIES. Edinburgh Journal of Botany. Cambridge University Press (CUP). doi:10.1017/s0960428609990266

Possible interface idea

Use DataTables to display the table of data.

Possible data publishing idea using Datasette

datasette provides an easy way to serve a SQLite database over the web. First generate the IPNI dump:

php dump-csv.php

Can use csvs-to-sqlite to convert CSV file to SQLite database:

csvs-to-sqlite ipni.csv ipni.db

Can then serve SQLite database from local machine:

datasette serve ipni.db

This then runs in local web browser. Can host remotely using now or Heroku, but that requires lots of hosts space for big datasets.

Can also make a Docker container:

datasette package ipni.db

This can take a little while as Docker assembles all the pieces, but if successful you should see something like this:

Successfully built b7f94292889c

In this case “b7f94292889c” is the container id, so it can be run, e.g.:

docker run -p 8081:8001 b7f94292889c

Could use the -t option to tag the container, e.g. (haven’t tried this yet)

datasette package -t rdmpage/ipni ipni.db
``

So, looks like a nice way to publish data that isn’t yet ready for a nice web app to go with it.

To push to docker first log in:

docker login -u -p


Then 

docker push rdmpage/ipni


## Note on beta IPNI

On 2018-01-19 I became aware of the [beta version of IPNI](http://beta.ipni.org) which looks nice and has a lot more DOI and BHL links.

## Progress

Progress to date (numbers of IPNI Ids mapped to a bibliographic identifier). There are 1,625,067 names in the working copy of IPNI.

Date: 2014-06-19

Identifier Number of names DOI 123,006 BioStor 29,066 BHL PageID 19,190 Any 158,387


Date: 2015-12-04

Identifier Number of names DOI 166,618 JSTOR 51,576 BioStor 30,681 BHL PageID 29,969 Any 249,529


Date: 2016-07-14

Identifier Number of names DOI 187,068 JSTOR 105,695 BioStor 43,627 BHL PageID 73,609 Any 360,917


## Browser

There is a simple PHP script index.php for a genus-level browser of the IPNI data (the full dataset isn't included in this repository).

## Dump

Dump IPNI (without bibliographic data)

## Examples

### One DOI encloses others

The DOI http://dx.doi.org/10.15553/c2012v671a12 **Notes on the Flora of Madagascar, 22–25** has the page span 137–151, but each note within the span has its own DOI (e.g., **Notes on the Genus Ochna L. (Ochnaceae) in Madagascar No Access** http://dx.doi.org/10.15553/c2012v671a14 ). This violates assumption that article spans are disjoint (or may intersect on the start and end pages).


## Linking to ORCID

In progress

## Taxonomic examples

*Dinebra decipiens* (DOI 10.1093/aob/mcs077, linked to one ORCID), GBIF has as *Leptochloa decipiens* http://www.gbif.org/species/2703867/, link made by OTT https://tree.opentreeoflife.org/opentree/argus/ottol@724661/Dinebra

## IPNI errors

### Mullaghera
*Mullaghera communis* 509328-1 (and other species in this genus) are linked to Oesterr. Bot. Z. 49:509, etc., but the pages don’t exist. *Mullaghera communis* was published by P. Bubani here: http://biodiversitylibrary.org/page/10609741, see also Index Kewensis http://biodiversitylibrary.org/page/42364805