Assessing Descriptive Substance in Free-Text Collection-Level Metadata

Collection-level metadata has the potential to provide important information about the features and purpose of individual collections. This paper reports on a content analysis of collection records in an aggregation of cultural heritage collections. The findings show that the free-text Description field often provides more accurate and complete representation of subjects and object types than the specified fields. Properties such as importance, uniqueness, comprehensiveness, provenance, and creator are articulated, as well as other vital contextual information about the intentions of a collector and the value of a collection, as a whole, for scholarly users. The results demonstrate that the semantically rich free-text Description field is essential to understanding the context of collections in large aggregations and can serve as a source of data for enhancing and customizing controlled vocabulariesIMLS NLG Research and Demonstration grant LG-06-07-0020-07published or submitted for publicationis peer reviewe

Dublin Core Metadata Harvested Through OAI-PMH

The introduction in 2001 of the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) increased interest in and awareness of metadata quality issues relevant to digital library interoperability and the use of harvested metadata to build "union catalogs" of digital information resources. Practitioners have offered wide-ranging advice to metadata authors and have suggested metrics useful for measuring the quality of shareable metadata. Is there evidence of changes in metadata practice in response to such advice and/or as a result of an increased awareness of the importance of metadata interoperability? This paper looks at metadata records created over a six-year period that have been harvested by the University of Illinois at Urbana Champaign, and reports on quantitative and qualitative analyses of changes observed over time in shareable metadata quality.IMLS National Leadership Grant LG-02-02-0281published or submitted for publicationis peer reviewe

Metadata Maker

Metadata Maker was developed to improve the productivity of cataloging and metadata workflows, allowing anyone to create metadata in various formats, regardless of their familiarity and experience with metadata standards.Ope

Metadata Maker for Digital Publication

As many academic and research libraries are considering or have already started developing digital scholarly publishing programs, these programs need to find a proper way to create metadata for access to these new publications. However, metadata for digital publications has its own challenges in two areas: metadata schemas and controlled vocabularies. For example, metadata for digital publications requires a specific set of metadata elements that are different from traditional print resources. Also, in order for scholarly digital publications to be managed and discovered with other books that are published by established publishing houses, the application of subject headings should be described using controlled vocabularies that are standard in the publishing community, such as BISAC (https://www.bisg.org/bisac/bisac-subject-codes), and represented in the ONIX format in addition to MARC and MODS, metadata schemas used in the library domain. Furthermore, as libraries are moving forward towards the semantic web and linked data, metadata should also include linked data components that would increase the discoverability of resources on the web. This poster introduces a metadata creation tool for electronic resources including digital publications, Metadata Maker for E-books (http://quest.library.illinois.edu/marcmaker/ebooks/) created to support these needs. The tool utilizes two subject headings: FAST for traditional library description, and BISAC subject codes and terms for publishers. Metadata Maker provides users, who may have minimal metadata knowledge and experience, a tool to create metadata in five different formats: MARC, MARCXML, MODS, schema.org embedded HTML, and ONIX for Books, depending on their needs.Ope

Disambiguating Descriptions: Mapping Digital Special Collections Metadata into Linked Open Data Formats

In this poster we describe the Linked Open Data (LOD) for Digital Special Collections project at the University of Illinois at Urbana-Champaign and describe some of the particular challenges that legacy metadata poses for representation in LOD formats. LOD formats are primarily based on the World Wide Web Consortium’s Resource Description Framework standard which demands both that entities be named by opaque universal identifiers whenever possible but also that metadata descriptions for entities be as unambiguous as possible. The challenges for disambiguating those descriptions are illustrated through examples drawn from digital special collections based at four different digital librariesOpe

Aligning author-supplied keywords for ETDs with domain-specific controlled vocabularies

Subject access can provide essential points of access for users to find, identify, select, and obtain various resources available in libraries. Subject access is not always available, however, due to the increasing amount of metadata created by non-catalogers (including author-supplied metadata), changes in libraries’ discovery services, and a lack of best practices for aligning non-controlled vocabularies to authorized subject headings. This paper addresses the issue of author-supplied metadata, specifically how to align keywords submitted by authors of electronic theses and dissertations (ETDs) with Library of Congress Subject Headings (LCSH) and discipline-specific taxonomies by analyzing 32,696 keywords from 5,365 master's theses and doctoral dissertations submitted to the University of Illinois at Urbana-Champaign's institutional repository between 2010 and 2014. This paper shares findings from the data analysis, including that matching rates vary depending on college, with newer or rapidly-developing fields (such as the School of Molecular and Cellular Biology) having lower matching rates than traditional, well-established fields of study (such as the College of Agriculture, Consumer, and Environmental Sciences), and recommends that when keyword reconciliation is performed, it should be done with more than one authority in tandem for the best results; when the LCSH and discipline-specific controlled vocabularies were combined, matching results were slightly or moderately increased.Ope

Exploring the Benefits for Users of Linked Open Data for Digitized Special Collections, White paper #1: Transforming special collections metadata into linked open data: mappings, entity reconciliation, workflows implemented & lessons learned

Transforming and migrating legacy metadata for special collections to a linked data compatible ontology requires metadata remediation, enhancement, and mapping. Entity reconciliation (adding the links) is a critical component as well. The first part of this white paper summarizes the mappings and workflows developed for our three digital special collections (Motley Collection of Theatre and Costume Design, Portraits of Actors, and the Kolb-Proust Archive Research), the challenges encountered, and solutions identified for these challenges. The second part of this white paper describes entity reconciliation approaches used to discover links to more information about the entities mentioned in the metadata.Andrew W. Mellon Foundation Award No. 31500650Ope

A Genetic and Structural Study of Genome Rearrangements Mediated by High Copy Repeat Ty1 Elements

Ty elements are high copy number, dispersed repeated sequences in the Saccharomyces cerevisiae genome known to mediate gross chromosomal rearrangements (GCRs). Here we found that introduction of Ty912, a previously identified Ty1 element, onto the non-essential terminal region of the left arm of chromosome V led to a 380-fold increase in the rate of accumulating GCRs in a wild-type strain. A survey of 48 different mutations identified those that either increased or decreased the rate of Ty-mediated GCRs and demonstrated that suppression of Ty-mediated GCRs differs from that of both low copy repeat sequence- and single copy sequence-mediated GCRs. The majority of the Ty912-mediated GCRs observed were monocentric nonreciprocal translocations mediated by RAD52-dependent homologous recombination (HR) between Ty912 and a Ty element on another chromosome arm. The remaining Ty912-mediated GCRs appeared to involve Ty912-mediated formation of unstable dicentric translocation chromosomes that were resolved by one or more Ty-mediated breakage-fusion-bridge cycles. Overall, the results demonstrate that the Ty912-mediated GCR assay is an excellent model for understanding mechanisms and pathways that suppress genome rearrangements mediated by high copy number repeat sequences, as well as the mechanisms by which such rearrangements occur

Histone H3K56 Acetylation, CAF1, and Rtt106 Coordinate Nucleosome Assembly and Stability of Advancing Replication Forks

Chromatin assembly mutants accumulate recombinogenic DNA damage and are sensitive to genotoxic agents. Here we have analyzed why impairment of the H3K56 acetylation-dependent CAF1 and Rtt106 chromatin assembly pathways, which have redundant roles in H3/H4 deposition during DNA replication, leads to genetic instability. We show that the absence of H3K56 acetylation or the simultaneous knock out of CAF1 and Rtt106 increases homologous recombination by affecting the integrity of advancing replication forks, while they have a minor effect on stalled replication fork stability in response to the replication inhibitor hydroxyurea. This defect in replication fork integrity is not due to defective checkpoints. In contrast, H3K56 acetylation protects against replicative DNA damaging agents by DNA repair/tolerance mechanisms that do not require CAF1/Rtt106 and are likely subsequent to the process of replication-coupled nucleosome deposition. We propose that the tight connection between DNA synthesis and histone deposition during DNA replication mediated by H3K56ac/CAF1/Rtt106 provides a mechanism for the stabilization of advancing replication forks and the maintenance of genome integrity, while H3K56 acetylation has an additional, CAF1/Rtt106-independent function in the response to replicative DNA damage

Frequent Occurrence of Mitochondrial DNA Mutations in Barrett’s Metaplasia without the Presence of Dysplasia

BACKGROUND: Barrett's esophagus (BE) is one of the most common premalignant lesions and can progress to esophageal adenocarcinoma (EA). The numerous molecular events may play a role in the neoplastic transformation of Barrett's mucosa such as the change of DNA ploidy, p53 mutation and alteration of adhesion molecules. However, the molecular mechanism of the progression of BE to EA remains unclear and most studies of mitochondrial DNA (mtDNA) mutations in BE have performed on BE with the presence of dysplasia. METHODS/FINDINGS: Thus, the current study is to investigate new molecular events (Barrett's esophageal tissue-specific-mtDNA alterations/instabilities) in mitochondrial genome and causative factors for their alterations using the corresponding adjacent normal mucosal tissue (NT) and tissue (BT) from 34 patients having Barrett's metaplasia without the presence of dysplasia. Eighteen patients (53%) exhibited mtDNA mutations which were not found in adjacent NT. mtDNA copy number was about 3 times higher in BT than in adjacent NT. The activity of the mitochondrial respiratory chain enzyme complexes in tissues from Barrett's metaplasia without the presence of dysplasia was impaired. Reactive oxygen species (ROS) level in BT was significantly higher than those in corresponding samples. CONCLUSION/SIGNIFICANCE: High ROS level in BT may contribute to the development of mtDNA mutations, which may play a crucial role in disease progression and tumorigenesis in BE