D73report

From Scratchpad Wiki
Jump to: navigation, search

Contents

D7.3 - Literature search

Due
31 October 2013
Delivered
23 October 2013†
Purpose
To enable a bibliography of life.
Benefit
Enables taxonomists to accurately and easily cite references.

† The date recorded here is when the deliverable report was written

Introduction

The Bibliography of Life draws on two ViBRANT deliverables. The current deliverable, D7.3 - Literature search, is realised as ReFinder. The year one deliverable, D7.1 - Community contributed bibliography, is realised as RefBank. Together these two deliverables enable us to provide breadth of coverage (ReFinder) and depth of coverage (RefBank) of biodiversity literature references.

RefBank

RefBank provides the underlying storage mechanism on which to build the Bibliography of Life.

For more information on RefBank as delivered in year one of ViBRANT see http://vbrant.eu/sites/vbrant.eu/files/D7-1_report_final.pdf.

Reflecting ViBRANT's agile approach to project management, milestone M7.15 - Define further milestones in the light of usage and feedback defined further milestones to fully integrate RefBank into the needs of the biodiversity community. The milestones are documented below at D73report#Milestones contributing to this deliverable. The success of this deliverable depended on these milestones.

A crucial aspect of RefBank is that it provides a set of curated references to anchor the results of a literature search. When searching across the many available sources, duplicate results will be produced because the same document is referenced in each source. RefBank offers a means to identify the canonical version of a reference, documented in M7.19 - Review of pilot of reference de-duplication software.

RefBank fits seamlessly into a researcher's workflow. All bibliographic contributions to Scratchpads are harvested automatically and available for searching through ReFinder. Similarly, all publications of Pensoft through the Pensoft Writing Tool are harvested automatically not only for their own reference but for the citations they contain, which are then stored in RefBank. Hence, these citations too are available for wider discovery by the community through ReFinder.

ReFinder

ReFinder, the output of this deliverable, provides the overlying search mechanism by which to exploit the Bibliography of Life.

Reflecting ViBRANT's agile approach to project management, this deliverable has been adapted to meet the evolving needs of the project and the biodiversity research community. Originally conceived as Task 7.4 Web service for search and information retrieval, that task was deprecated and agreed to be delivered instead through restructured tasks 7.1 and 7.2 (See year one annual report for more details.)

The deliverable has finally been realised as a portal to expand the scope of the community contributed literature captured by RefBank to encompass generic bibliographic resources.

Using ReFinder

This section describes how to use ReFinder. Firstly from the perspective of an end-user, and secondly from the perspective of a developer.

From a screen

The following screenshots take you through using ReFinder as an end-user would, sat in front of a screen.

(thumbnail)
Screenshot of ReFinder search page.


Screenshot of ReFinder search page.

This is the blank search page that is presented to a user. Various fields are present to support either a simple search, using the free text field, or an advanced search, using one of the specific fields such as author. Multiple fields can be used in an advanced search.

(thumbnail)
Screenshot of ReFinder search page, with search results.


Screenshot of ReFinder search page, with search results.

This is a typical list of results presented to a user. In this case, a search using two terms, author and year, was invoked.

(thumbnail)
Screenshot of ReFinder search page, with citation options.


Screenshot of ReFinder search page, with citation options.

Hovering the mouse pointer over an individual search result highlights it, and activates the option to select it for download in a variety of formats. The Bibliography of Life supports over 600 citation styles.

(thumbnail)
Screenshot of ReFinder search page, with downloadable citation.


Screenshot of ReFinder search page, with downloadable citation.

Here we see another results from the same query, this time with the formatted citation ready to be copied by the user into their document.

From a program

ReFinder accepts GET requests in a RESTful manner. They are documented in the online API page (see #refinderapi screenshot below).

Three examples are shown here, first using PHP and then using Python to invoke ReFinder. The examples are:

  • a simple search that uses only the plain text field, in this case we constrain the search to RefBank and return three results only
  • an advanced search enabling us to specify, in this example, author and year values; this search is also limited to three results
  • a simple search across all eligible databases using a known doi, particularly useful for a targeted search

PHP examples of invoking ReFinder:

<?php
echo "\n-------\nresult of ReFinder simple search\n";
$results = file_get_contents('http://refinder.org/find?search=simple&db=refbank&limit=3&text=Penev');
echo $results;
echo "\n-------\nresult of ReFinder author and year search\n";
$results = file_get_contents('http://refinder.org/find?search=advanced&limit=3&author=Penev&year=2012');
echo $results;
echo "\n-------\nresult of ReFinder doi search\n";
$results = file_get_contents('http://refinder.org/find?search=simple&text=PMC3234428');
echo $results;
echo "\n-------\n";
?>

Python examples of invoking ReFinder:

import urllib.parse
import urllib.request
 
req = urllib.request.Request(url='http://refinder.org/find?search=simple&db=refbank&limit=3&text=Penev')
f = urllib.request.urlopen(req)
print('\n-----\nresult of ReFinder simple search')
print(f.read().decode('utf-8'))
 
req = urllib.request.Request('http://refinder.org/find?search=advanced&limit=3&author=Penev&year=2012')
f = urllib.request.urlopen(req)
print('\n-----\nresult of ReFinder author and year search')
print(f.read().decode('utf-8'))
 
req = urllib.request.Request('http://refinder.org/find?search=simple&text=PMC3234428')
f = urllib.request.urlopen(req)
print('\n-----\nresult of ReFinder doi search')
print(f.read().decode('utf-8'))

Bibliography of Life on the web

This section briefly covers the Bibliography of Life's web presence.

(thumbnail)
Screenshot of Bibliography of Life home page.


Screenshot of Bibliography of Life home page, http://biblife.org/

This is a simple home page, that will continue after the completion of ViBRANT, and provides a single reference point for all aspects of the Bibliography of Life. As can be seen, it takes the form of an open book, with the two components taking up one page each. Following the links gives more detailed information about the components. By way of example, below three screenshots are shown for each component:

  • the home page, a simple description
  • the about page, setting out the benefits of using the component
  • the API page, describing how to interact with the component programatically.

Other pages cover installation instructions, access to the source code and contact information.

Bibliography of life component: RefBank

(thumbnail)
Screenshot of RefBank home page.


Screenshot of RefBank home page, http://refbank.org/

(thumbnail)
Screenshot of RefBank about page.


Screenshot of RefBank about page, http://refbank.org/about.html

(thumbnail)
Screenshot of RefBank API documentation page.


Screenshot of RefBank API documentation page, http://refbank.org/api.html

Bibliography of life component: ReFinder

(thumbnail)
Screenshot of ReFinder home page.


Screenshot of ReFinder home page, http://refinder.org/

(thumbnail)
Screenshot of ReFinder about page.


Screenshot of ReFinder about page, http://refinder.org/about.html

(thumbnail)
Screenshot of ReFinder API documentation page.


Screenshot of ReFinder API documentation page, http://refinder.org/api.html

Milestones contributing to this Deliverable

This section lists the many milestones that contributed to the development of this deliverable.

For more detail about each milestone and its contribution follow the link to the milestone's report.

M7.21 Add metadata to cover origin of bibliographies

Completed Wed, 11/04/2012 http://www.wiki.scratchpads.eu/w/M721report

M7.22 Import bibliographies from Pensoft to RefBank

Completed Tue, 08/05/2012 http://www.wiki.scratchpads.eu/w/M722report

M7.23 Extend RefBank import routines to support other widely used bibliographic formats, eg BibTex, RIS, etc

Completed Thu, 31/05/2012 http://www.wiki.scratchpads.eu/w/M723report

M7.24 Upload service for complete bibliographies

Completed Thu, 31/05/2012 http://www.wiki.scratchpads.eu/w/M724report

M7.25 Enhance reference parser to parse references in bulk uploads

Completed Tue, 30/10/2012 http://www.wiki.scratchpads.eu/w/M725report

M7.19 - Review of pilot of reference de-duplication software

Completed Tue, 30/07/2013 http://www.wiki.scratchpads.eu/w/M719Report

M7.20 - Workpackage software documentation produced

Completed Wed, 23/10/2013 http://www.wiki.scratchpads.eu/w/M720Report

M7.26 – Workpackage software packaged

Completed Wed, 23/10/2013 http://www.wiki.scratchpads.eu/w/M726report

M7.27 – Publish ViBRANT NLP corpus

Completed Thu, 24/10/2013 http://www.wiki.scratchpads.eu/w/M727report

M7.18 - First integration phase complete

Due Fri, 15/11/2013

Publicity and dissemination

The completed Bibliography of Life with its two components was demonstrated successfully at two large conferences in October 2013: BIH2013 and TDWG2013.

Each conference was attended by several hundred researchers working variously at the intersection of biodiversity and informatics, drawn from around the world.

For each conference posters were produced to advertise the demonstrations. The posters have been placed in ViBRANT's Scratchpad as outputs, and are available for BIH2013 and TDWG2013 respectively.

In addition, the Bibliography of Life featured in a workshop at BIH2013, bibliographies in a changing landscape, drawing interested questions from developers and users of bibliographic tools.

Sustainability

We have secured the continued support and development of the Bibliography of Life and its two components after the completion of ViBRANT. This is documented as part of the ViBRANT deliverable D2.3 - Financial sustainability, in its report.

Workpackages
EMonocot
Personal tools