Data Curation Task
- AKA: Curation, Curating, Data Curation, Curation Task, Curating Task, Curational Process, Digital Curation.
- See: Annotation Task, Data Provenance Task, Entity Mention.
- … 3. (databases) The manual updating of information in a database.
- Digital curation, broadly interpreted, is about maintaining and adding value to a trusted body of
digital information for current and future use.
- (Cusick et al., 2009) ⇒ Michael E Cusick, Haiyuan Yu, Alex Smolyar, Kavitha Venkatesan, Anne-Ruxandra Carvunis, Nicolas Simonis, Jean-François Rual, Heather Borick, Pascal Braun, Matija Dreze, Jean Vandenhaute, Mary Galli, Junshi Yazaki, David E Hill, Joseph R Ecker, Frederick P Roth, and Marc Vidal. (2009). “Literature-Curated Protein Interaction Datasets.” In: Nature Methods 6, 39 - 46 (2009)
- Our findings of large error rates in curated protein interaction databases, at least for yeast and human, are consistent with recent hints that the quality of literature-curated datasets may not be as high as widely perceived23,29,43–45. Perhaps occasionally curator error is responsible. However, we suggest that the errors are due not so much to curators but to the simple reality that extracting accurate information from a long free-text document can be extremely difficult. Gene name confusion is particularly thorny30,46. An example from our curated yeast sample illustrates the difficulties. A purification with a tandem affinity purification tag with Vps71/Swc6 (slash separates synonymous approved names) as bait47 pulls down a protein named Swc3, but double-checking this finds that the coresponding open reading frame is actually SWC3 (locus name YAL011w), and not the ALR1/SWC3 (locus name YOL130w) open reading frame curated in the database. A shared synonym thoroughly muddled the curation.
- (Howe et al., 2008) ⇒ Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White, and Seung Yon Rhee. (2008). “Big Data: The future of biocuration.” In: Nature, 455.
- Curation (Biology): curation of biological databases in this context means basically the manual extraction of biological information from the literature by a domain expert. The aim is to transform information contained in free text (scientific literature) to information stored in form of a structured database record (biological databases).
- What is Digital Curation?: Digital curation, broadly interpreted, is about maintaining and adding value to a trusted body of digital information for current and future use. The digital archiving and preservation community now looks beyond the preservation, cataloguing and cross referencing of static digital objects such as documents. The scientific community has data characterised by structure, volatility and scale. These require us to extend our notions of curation. We must also investigate the principles that underlie appraisal, and lessons learnt about the economics of preservation.