Robert E. Belford

WikiHyperGlossary (WHG): an information literacy technology for chemistry documents

BackgroundThe WikiHyperGlossary is an information literacy technology that was created to enhance reading comprehension of documents by connecting them to socially generated multimedia definitions as well as semantically relevant data. The WikiHyperGlossary enhances reading comprehension by using the lexicon of a discipline to generate dynamic links in a document to external resources that can provide implicit information the document did not explicitly provide. Currently, the most common method to acquire additional information when reading a document is to access a search engine and browse the web. This may lead to skimming of multiple documents with the novice actually never returning to the original document of interest. The WikiHyperGlossary automatically brings information to the user within the current document they are reading, enhancing the potential for deeper document understanding.ResultsThe WikiHyperGlossary allows users to submit a web URL or text to be processed against a chosen lexicon, returning the document with tagged terms. The selection of a tagged term results in the appearance of the WikiHyperGlossary Portlet containing a definition, and depending on the type of word, tabs to additional information and resources. Current types of content include multimedia enhanced definitions, ChemSpider query results, 3D molecular structures, and 2D editable structures connected to ChemSpider queries. Existing glossaries can be bulk uploaded, locked for editing and associated with multiple social generated definitions.ConclusionThe WikiHyperGlossary leverages both social and semantic web technologies to bring relevant information to a document. This can not only aid reading comprehension, but increases the users’ ability to obtain additional information within the document. We have demonstrated a molecular editor enabled knowledge framework that can result in a semantic web inductive reasoning process, and integration of the WikiHyperGlossary into other software technologies, like the Jikitou Biomedical Question and Answer system. Although this work was developed in the chemical sciences and took advantage of open science resources and initiatives, the technology is extensible to other knowledge domains. Through the DeepLit (Deeper Literacy: Connecting Documents to Data and Discourse) startup, we seek to extend WikiHyperGlossary technologies to other knowledge domains, and integrate them into other knowledge acquisition workflows.

On the Realm of Virtual Colloquium

The nature of scientific communications is evolving in the digital age, and leveraging emerging technologies presents ongoing challenges and opportunities to an international scientific society like IUPAC. One of the missions of the Union is to contribute to the advancement of science by enabling communication among scientists across national, cultural, and linguistic boundaries. Historically, there have been two modes to this mission. First, IUPAC is responsible for standardizing the metrics and terminologies pursuant to effective communication among chemists. Second, it disseminates ideas and information through traditional modes of communication, including physical or face-to-face meetings and printed communications. For some time now, digital information and communications technologies have been impacting the traditional modes of communication, while also enabling new ones through the instant transference of actual experimental data, adding a whole new layer to the needs for non-linguistic data standards. In this paper, we will explore these questions, focus on the former challenges, and report on a Virtual Colloquium on IYC2011 which ran concomitant with the ICCE-ECRICE 2012.

ConfChem Conference on Select 2016 BCCE Presentations: Twentieth Year of the OLCC

The ACS CHED Committee on Computers in Chemical Education (CCCE) ran the first intercollegiate OnLine Chemistry Course (OLCC) on Environmental and Industrial Chemistry in 1996, and is offering the seventh OLCC on Cheminformatics and Public Compound Databases: An Introduction to Big Data in Chemistry in 2017. This Communication summarizes the past, present, and future of OLCCs, which evolved out of the online ConfChem conferences that the CCCE has run since 1993. OLCCs actually pioneered the use of HTML papers before ConfChem did, as well as enabled discussions centered on different sections of a paper. OLCCs are technically hybrid courses involving local faculty facilitators who meet face-to-face with students and online guest lecturers who are experts in the topic of the OLCC. These not only allow schools to offer courses on topics they may not normally be able to offer, but open up the opportunity for collaborative teaching and learning across multiple institutions, both academic and nonacademic. This C...

Review of Chasing Molecules: Poisonous Products, Human Health, and the Promise of Green Chemistry

I her book, Chasing Molecules: Poisonous Products, Human Health, and the Promise of Green Chemistry, the investigative journalist Elizabeth Grossman discusses the ongoing environmental and health issues associated with our society’s massive production of synthetic chemicals over the last half-century. In addition to these issues, this book covers the implications of how synthetic chemists perform science, and introduces the concept of green chemistry. The book is 249 pages long, has 10 chapters and 289 footnotes. It is appropriate reading for a wide audience, ranging from the general public to practicing scientists. A table of the acronyms and abbreviations would have been an asset. Some minor mistakes are evident, such as identifying perchlorates as VOCs (p 15), but these do not take away from the value of the book. Throughout this book Grossman interviews an impressive array of scientists, through whose expertise, in addition to her own investigative work, she presents her message.

ISDB: Interaction Sentence Database

BackgroundRapid growth in the scientific literature available on-line continues to motivate shifting data analysis from humans to computers. For example, greater knowledge of sentence characteristics indicative of interaction between two biological entities is needed to aid in the creation of better-performing information extraction tools for effectively using this rich body of information.FindingsThe Interaction Sentence Database (ISDB) allows users to retrieve sets of sentences fitting specified characteristics. To support this, a database of sentences from abstracts in MEDLINE was created. The sentences in the database all contain at least two biomolecule terms and one interaction-indicating term. A web interface to the database allows the user to query for sentences containing an interaction-indicating term, a single biomolecule name, or two biomolecule names, as well as for a list of biomolecules co-occurring with a given biomolecule in at least one sentence.ConclusionsThe system supports researchers needing conveniently available sets of sample sentences for corpus-based research on sentence properties. It also illustrates a model architecture for a sentence-based retrieval system which would be useful to people seeking information and knowledge on-line. ISDB can be freely accessed over the Web at http://bioinformatics.ualr.edu/cgi-bin/services/ISDB/isdb.cgi, and the processed database will be provided upon request.

Conquering the Content:: A Step-by-Step Guide to Online Course Design

This book covers general principles in online course design but is written as a guide to assist an instructor in developing an online course that incorporates those principles.