Searcharxiv⌕ Search

arXiv subjects

Jane Greenberg

Publications and source records attributed to Jane Greenberg.

24 records · Page 2Linked to original sources

Text to Insight: Accelerating Organic Materials Knowledge Extraction via Deep Learning

Scientific literature is one of the most significant resources for sharing knowledge. Researchers turn to scientific literature as a first step in designing an experiment. Given the extensive and growing volume of literature, the common approach of reading and manually extracting knowledge is too time consuming, creating a bottleneck in the research cycle. This challenge spans nearly every scientific domain. For the materials science, experimental data distributed across millions of publications are extremely helpful for predicting materials properties and the design of novel materials. However, only recently researchers have explored computational approaches for knowledge extraction primarily for inorganic materials. This study aims to explore knowledge extraction for organic materials. We built a research dataset composed of 855 annotated and 708,376 unannotated sentences drawn from 92,667 abstracts. We used named-entity-recognition (NER) with BiLSTM-CNN-CRF deep learning model to automatically extract key knowledge from literature. Early-phase results show a high potential for automated knowledge extraction. The paper presents our findings and a framework for supervised knowledge extraction that can be adapted to other scientific domains.

cs.CL↗

Project Pipeline: Preservation, Persistence, and Performance

Preservation pipelines demonstrate extended value when digitized content is also computation ready. Expanding this to historical controlled vocabularies published in analog format requires additional steps if they are to be fully leveraged for research. This paper reports on work addressing this challenge. We report on a pipeline and project progress addressing three key goals: 1) transforming the 1910 Library of Congress Subject Headings (LCSH) to the Simple Knowledge Organization System (SKOS) linked data standard, 2) implementing persistent identifiers (PIDs) and launching our prototype ARK resolver, and 3) importing the 1910 LCSH into the Helping Interdisciplinary Vocabulary Engineering (HIVE) System to support automatic metadata generation and scholarly analysis of the historical record. The discussion considers the implications of our work in the broader context of preservation, and the conclusion summarizes our work and identifies next steps.

cs.DL↗

The role of metadata in reproducible computational research

Reproducible computational research (RCR) is the keystone of the scientific method for in silico analyses, packaging the transformation of raw data to published results. In addition to its role in research integrity, RCR has the capacity to significantly accelerate evaluation and reuse. This potential and wide-support for the FAIR principles have motivated interest in metadata standards supporting RCR. Metadata provides context and provenance to raw data and methods and is essential to both discovery and validation. Despite this shared connection with scientific data, few studies have explicitly described the relationship between metadata and RCR. This article employs a functional content analysis to identify metadata standards that support RCR functions across an analytic stack consisting of input data, tools, notebooks, pipelines, and publications. Our article provides background context, explores gaps, and discovers component trends of embeddedness and methodology weight from which we derive recommendations for future work.

cs.DL↗

HIVE-4-MAT: Advancing the Ontology Infrastructure for Materials Science

Introduces HIVE-4-MAT - Helping Interdisciplinary Vocabulary Engineering for Materials Science, an automatic linked data ontology application. Covers contextual background for materials science, shared ontology infrastructures, and reviews the knowledge extraction and indexing process. HIVE-4-MAT's vocabulary browsing, term search and selection, and knowledge extraction and indexing are reviewed, and plans to integrate named entity recognition. Conclusion highlights next steps with relation extraction to support better ontologies.

cs.DL↗

A Computational Approach to Historical Ontologies

This paper presents a use case exploring the application of the Archival Resource Key (ARK) persistent identifier for promoting and maintaining ontologies. In particular, we look at improving computation with an in-house ontology server in the context of temporally aligned vocabularies. This effort demonstrates the utility of ARKs in preparing historical ontologies for computational archival science.

cs.DL↗

Data objects and documenting scientific processes: An analysis of data events in biodiversity data papers

The data paper, an emerging scholarly genre, describes research datasets and is intended to bridge the gap between the publication of research data and scientific articles. Research examining how data papers report data events, such as data transactions and manipulations, is limited. The research reported on in this paper addresses this limitation and investigated how data events are inscribed in data papers. A content analysis was conducted examining the full texts of 82 data papers, drawn from the curated list of data papers connected to the Global Biodiversity Information Facility (GBIF). Data events recorded for each paper were organized into a set of 17 categories. Many of these categories are described together in the same sentence, which indicates the messiness of data events in the laboratory space. The findings challenge the degrees to which data papers are a distinct genre compared to research papers and they describe data-centric research processes in a through way. This paper also discusses how our results could inform a better data publication ecosystem in the future.

cs.DL↗