Wormbase Curation Interfaces and Tools

Curating biological information from the published literature can be time- and labor-intensive especially without automated tools. WormBase1 has adopted several curation interfaces and tools, most of which were built in-house, to help curators recognize and extract data more efficiently from the literature. These tools range from simple computer interfaces for data entry to employing scripts that take advantage of complex text extraction algorithms, which automatically identify specific objects in a paper and presents them to the curator for curation. By using these in-house tools, we are also able to tailor the tool to the individual needs and preferences of the curator. For example, Gene Ontology Cellular Component and gene-gene interaction curators employ the text mining software Textpresso2 to indentify, retrieve, and extract relevant sentences from the full text of an article. The curators then use a web-based curation form to enter the data into our local database. For transgene and antibody curation, curators use the publicly available Phenote ontology annotation curation interface (developed by the Berkeley Bioinformatics Open-Source Projects (BBOP)), which we have adapted with datatype specific configurations. This tool has been used as a basis for developing our own Ontology Annotator tool, which is being used by our phenotype and gene ontology curators. For RNAi curation, we created web-based submission forms that allow the curator to efficiently capture all relevant information. In all cases, the data undergoes a final scripted data dump step to make sure all the information conforms into a readable file by our object oriented database

Practices of Remembrance: The Experiences of Artists and Curators in the Centenary Commemoration of World War I

The centenary of World War One was marked in the UK by an unprecedented national investment in the creative arts as a vehicle for remembrance. This scale of funding for commemorative arts, not least under a government whose mantra had been economic “austerity”, demonstrates the importance that the nation-state placed on remembrance and on engaging the public in acts of memory through the arts. In the aftermath of the centenary, funding bodies have commissioned evaluations of this programming. These evaluations have focused on audiences reached, organisations benefitted, and social transformation. What remain occluded by the reports are the experiences of the artists themselves and the curators with whom they worked. In this article I explore the personal and affective experiences of several artists and curators whose work contributed to this national programme of remembrance. I ask: to what extent did artists and curators consciously engage with prior artistic responses to World War One? How did the context of collective commemoration and memory-making inform their practice and the works produced? What did their involvement in this programme of national remembrance make them feel? What were the narratives of the war they wanted to tell? To begin to answer these questions, I draw on a series of one-to-one interviews conducted with a number of artists and curators who were involved in commemorative projects in the UK and overseas

Art Museum Curators and Management

Art museums house the greatest works from artists around the world from classics to modern pop art, without discrimination and open to interpretation. Art museums are debatably one of the most sacred places in society. Any history museum will give details about ancient artifacts or new discoveries; art, however, can change in meaning with each new visitor. Museum curators go beyond the “do not touch” signs with their large key rings opening vaults of worth and beauty. Curators work directly with artists and other museums to resurrect a dying cultural tradition. With the assistance of Valparaiso University’s own Gloria Ruff, Assistant Curator and Registrar, I have had the privilege to get a guided tour of what goes on in a day in the life of a curator. Museums are in decline, maintaining with their heads just above the water. Laws were passed and curriculums changed in higher education so that these houses of culture do not dissipate into the history books

eBEAC: electronic Bulletin board for European Avian Curators

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UbiComp in Opportunity Spaces: Challenges for Participatory Design

The rise of ubiquitous computing (UbiComp), where pervasive, wireless and disappearing technologies offer hitherto unavailable means of supporting activity, increasingly opens up ‘opportunity spaces’. These are spaces where there is no urgent problem to be solved, but much potential to augment and enhance practice in new ways. Based on our experience of co-designing novel user experiences for visitors to an English country estate, we discuss challenges for PD in such an opportunity space. Key amongst these are how to build a working relationship of value when there are no urgent requirements; how to understand and scope the space of opportunities; and how to leave users with new resources of value to them

Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation

Background: Manual curation of experimental data from the biomedical literature is an expensive and time-consuming endeavor. Nevertheless, most biological knowledge bases still rely heavily on manual curation for data extraction and entry. Text mining software that can semi- or fully automate information retrieval from the literature would thus provide a significant boost to manual curation efforts. Results: We employ the Textpresso category-based information retrieval and extraction system http://www.textpresso.org webcite, developed by WormBase to explore how Textpresso might improve the efficiency with which we manually curate C. elegans proteins to the Gene Ontology's Cellular Component Ontology. Using a training set of sentences that describe results of localization experiments in the published literature, we generated three new curation task-specific categories (Cellular Components, Assay Terms, and Verbs) containing words and phrases associated with reports of experimentally determined subcellular localization. We compared the results of manual curation to that of Textpresso queries that searched the full text of articles for sentences containing terms from each of the three new categories plus the name of a previously uncurated C. elegans protein, and found that Textpresso searches identified curatable papers with recall and precision rates of 79.1% and 61.8%, respectively (F-score of 69.5%), when compared to manual curation. Within those documents, Textpresso identified relevant sentences with recall and precision rates of 30.3% and 80.1% (F-score of 44.0%). From returned sentences, curators were able to make 66.2% of all possible experimentally supported GO Cellular Component annotations with 97.3% precision (F-score of 78.8%). Measuring the relative efficiencies of Textpresso-based versus manual curation we find that Textpresso has the potential to increase curation efficiency by at least 8-fold, and perhaps as much as 15-fold, given differences in individual curatorial speed. Conclusion: Textpresso is an effective tool for improving the efficiency of manual, experimentally based curation. Incorporating a Textpresso-based Cellular Component curation pipeline at WormBase has allowed us to transition from strictly manual curation of this data type to a more efficient pipeline of computer-assisted validation. Continued development of curation task-specific Textpresso categories will provide an invaluable resource for genomics databases that rely heavily on manual curation

Objects of desire: creating legacies, one collection at a time

Although their motivations might appear different, both individual collectors and museum curators seek to define themselves and leave their mark on the world through the things that they acquire.Collectors and collecting