Biodiversity literature mark-up Compelling use cases for Natural History Collections Dr Dimitris Koureas Natural History Museum London Workshop on mark-up of biodiversity literature Berlin February 2014 DimitrisKoureas

Use case 1: Assisted label transcription Use case 2: Measuring the impact of collections Who are the current stakeholders? Support from Societal actors? What are the direct societal benefits? Natural History Museums can be key players but… SO… > 260 million specimens Introduction Significant research effort has been invested Literature markup could have industry-wide applications with significant impact We need to demonstrate compelling use cases that will engage stakeholders

Legacy literature markup of specimen records can facilitate label transcription process Digital NH Museums -Digital is NH museums strategic decision Challenge 1 of i n the Science strategy of NHM -Collection digitisation is prioritised in all major museums NHM allocated c. £750k for the next three years (not including capital expenditure) -Label transcription is important but challenging Use case 1: Assisted label transcription

Manual transcription of label elements curators crowdsourcing Manual transcription of semantic units in the label OCR/markup (semi-) automatic Use case 1: Assisted label transcription Different approaches for label transcription Hybrid models are currently in use

High resolution Typewritten Well defined structure and semantic units Suitable label for OCR and markup vs Low resolution Handwritten No proper structure Not suitable label for OCR Use case 1: Assisted label transcription Current approaches for label transcription

Crowdsourcing Current approaches for label transcription Use literature markup to identify specimen records and match against the physical object In-house Literature assisted transcription Manual or semi-automated Slow and cost ineffective Not suitable for large collections Unpredictable outcome Data cleaning needed We can enhance current approaches by introducing Use case 1: Assisted label transcription

a 1/Li I ) vi5 5, {L I‘O SPXFS \9.E " ‘: 3P~‘’‘fl\ % A HERB. ORPHANIDEUM. 3‘_‘w:a 3 PummI “lift u’ f9 ‘ A ‘-*’ /1i. _ I -}Z_,,_‘;_’:£€ Cg‘?! ~ <‘:.g‘{x ATHU 3638 Basic OCR output Create a link between specimen and literature Label transcription: Don’t do the job twice! Most labels have already been transcribed in taxonomic literature Catalogue number Use case 1: Assisted label transcription Published in 2012

Literature assisted transcription Transcription of specimen labels Is being crowdsourced for the last 250 years Minimum need of data cleaning Specimen data from small collections around the world Specimens labels transcribed several times Label transcription: Don’t do the job twice! Most labels have already been transcribed in taxonomic literature Use case 1: Assisted label transcription

Value in itself Value through utilisation preservation curation Data extraction Digitisation Natural History Collections Openness Establishing through measuring the scientific and Societal impact of collections Use case 2: measuring NH collections impact Traditional activities of repositories McAlpine (1986): 12.7% of papers used collections & 44.4% made collections

Legacy literature markup Specimen identifiers specimen citation metrics webservice Collection assessment Use case 2: measuring NH collections impact Specimen metadata born digital literature

Tracking specimen citations in literature can 1.highlight important collections 2.Promote the value of smaller repositories 3.Steer digitisation efforts 4.Help in collection gap analysis 5.Attract more funding Use case 2: measuring NH collections impact

Some concerns: Tracking specimen records in literature means tracking references to physical objects DOIs could be the easiest way BUT we cannot assign DOIs to physical objects unless museums quickly proceed in creating comprehensive collection data portals and assign UI to all records Use case 2: measuring NH collections impact The use of persistent identifiers would help NH collection curators to track the scientific impact of their collections but

Compelling use cases for Natural History Collections Biodiversity literature mark-up: Beyond taxonomic names Workshop on mark-up of biodiversity literature Berlin February 2014 Thank