This document outlines a search of library databases and websites on the topic of hospital-acquired infections. A search of the internet using Google produced over 8.7 million results for "hospital-acquired infections" and narrowed results to 475,000 when searched with quotation marks. Credible websites like the CDC were evaluated. Database searches in CINAHL and Business Source Complete using advanced search techniques found relevant peer-reviewed articles on reducing infections through hand washing and estimating infection incidence and burden. Appendices provide screenshots of search results.
Powering Scientific Discovery with the Semantic Web (VanBUG 2014)Michel Dumontier
In the quest to translate the results biomedical research into effective clinical applications, many are now trying to make sense of the large and rapidly growing amount of public biomedical data. However, substantial challenges exist in traversing the currently fragmented data landscape. In this talk, I will discuss our efforts to use Semantic Web technologies to facilitate biomedical research through the formulation, publication, integration, and exploration of facts, expert knowledge, and web services.
Generating Biomedical Hypotheses Using Semantic Web TechnologiesMichel Dumontier
With its focus on investigating the nature and basis for the sustained existence of living systems, modern biology has always been a fertile, if not challenging, domain for formal knowledge representation and automated reasoning. Over the past 15 years, hundreds of projects have developed or leveraged ontologies for entity recognition and relation extraction, semantic annotation, data integration, query answering, consistency checking, association mining and other forms of knowledge discovery. In this talk, I will discuss our efforts to build a rich foundational network of ontology-annotated linked data, discover significant biological associations across these data using a set of partially overlapping ontologies, and identify new avenues for drug discovery by applying measures of semantic similarity over phenotypic descriptions. As the portfolio of Semantic Web technologies continue to mature in terms of functionality, scalability and an understanding of how to maximize their value, increasing numbers of biomedical researchers will be strategically poised to pursue increasingly sophisticated KR projects aimed at improving our overall understanding of the capability and behavior of biological systems.
With the recent announcement that GlaxoSmithKline have released a huge tranche of whole cell malaria screening data to the public domain, accompanied by a corresponding publication, this raises some issues for consideration before this exemplar instance becomes a trend. We have examined the data from a high level, by studying the molecular properties, and consider the various alerts presently in use by major pharma companies. We acknowledge the potential value of such data but also raise the issue of the actual value of such datasets released into the public domain. We also suggest approaches that could enhance the value of such datasets to the community and theoretically offer more immediate benefit to the search for leads for other neglected diseases.
Locating scientific government information on the webShannon Lynch
This is a 2017 Powerpoint presentation given at the Department of Interior Library. The sources and information were correct at the time of presentation but have not been updated and should be double checked for current accuracy. Please feel free to contact the Department of Interior Library with any questions.
Powering Scientific Discovery with the Semantic Web (VanBUG 2014)Michel Dumontier
In the quest to translate the results biomedical research into effective clinical applications, many are now trying to make sense of the large and rapidly growing amount of public biomedical data. However, substantial challenges exist in traversing the currently fragmented data landscape. In this talk, I will discuss our efforts to use Semantic Web technologies to facilitate biomedical research through the formulation, publication, integration, and exploration of facts, expert knowledge, and web services.
Generating Biomedical Hypotheses Using Semantic Web TechnologiesMichel Dumontier
With its focus on investigating the nature and basis for the sustained existence of living systems, modern biology has always been a fertile, if not challenging, domain for formal knowledge representation and automated reasoning. Over the past 15 years, hundreds of projects have developed or leveraged ontologies for entity recognition and relation extraction, semantic annotation, data integration, query answering, consistency checking, association mining and other forms of knowledge discovery. In this talk, I will discuss our efforts to build a rich foundational network of ontology-annotated linked data, discover significant biological associations across these data using a set of partially overlapping ontologies, and identify new avenues for drug discovery by applying measures of semantic similarity over phenotypic descriptions. As the portfolio of Semantic Web technologies continue to mature in terms of functionality, scalability and an understanding of how to maximize their value, increasing numbers of biomedical researchers will be strategically poised to pursue increasingly sophisticated KR projects aimed at improving our overall understanding of the capability and behavior of biological systems.
With the recent announcement that GlaxoSmithKline have released a huge tranche of whole cell malaria screening data to the public domain, accompanied by a corresponding publication, this raises some issues for consideration before this exemplar instance becomes a trend. We have examined the data from a high level, by studying the molecular properties, and consider the various alerts presently in use by major pharma companies. We acknowledge the potential value of such data but also raise the issue of the actual value of such datasets released into the public domain. We also suggest approaches that could enhance the value of such datasets to the community and theoretically offer more immediate benefit to the search for leads for other neglected diseases.
Locating scientific government information on the webShannon Lynch
This is a 2017 Powerpoint presentation given at the Department of Interior Library. The sources and information were correct at the time of presentation but have not been updated and should be double checked for current accuracy. Please feel free to contact the Department of Interior Library with any questions.
Searching for chemical information using PubChemSunghwan Kim
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (April 1, 2019). [CHED 303]
==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database, which provides information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically-modified) amino acid and nucleic acid sequences (including siRNA and miRNA). With three million unique users per month at peak, PubChem is ranked as one of the most visited chemistry websites in the world. A substantial number of PubChem users are between ages 18 and 24, who are likely to be undergraduate or graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. In this talk, we will present “PubChem Search”, a new web interface that allows users to quickly find desired chemical information. This interface supports chemical name search as well as various types of chemical structure search, including identity/similarity search, superstructure/substructure search, and molecular search. Using PubChem Search, it is also possible to search for journal articles or patent documents that mention a given chemical. The hits returned from a search can be downloaded to local machines or further refined or analyzed in conjunction with other PubChem tools and services. In this presentation, we will demonstrate how the PubChem Search interface can be used to search beyond google for chemical information of interest.
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.
PubChem: a public chemical information resource for big data chemistrySunghwan Kim
Presented at the Joint Statistical Meetings (JSM) 2020 (virtual) on August 3, 2020.
==== Abstract ====
The idea of “big data” has recently been drawing much attention of the scientific community as well as the general public. An example of big data in Chemistry is the data contained in PubChem, which is a public database of chemical substance descriptions and their biological activities at the National Institutes of Health. PubChem is a sizeable system with 235 million depositor-provided substance descriptions, 96 million unique chemical structures, 1.1 million biological assays, and 268 million biological activity result outcomes. It also contains significant amounts of scientific research data and the inter-relationships between chemicals, proteins, genes, scientific literature, patents and more. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering multi-target ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). This presentation provides an overview of how PubChem’s data, tools, and services can be used for bioassay data analysis and virtual screening (VS) and discusses important aspects of exploiting PubChem for drug discovery.
The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
Learn how to search VHL Search Portal:
- How to start a search?
- What is the methodology for an efficient search? (search question, define database, descriptors, identify keywords, search the databases);
- Check the standard search terms on DeCS;
- Checking the standard terms, search on VHL.
Learn how to identify what to look for when selecting resources; judge if information will be relevant for your assignments and recognise if a source is credible.
This presentation shares a 10 minute pitch of big data potentials in the field of life sciences as presented at the 2015 CMS Global Life Science Forum on Nov 9, 2015 in Frankfurt
Searching for chemical information using PubChemSunghwan Kim
Presented at the 257th American Chemical Society (ACS) National Meeting in Orlando, FL (April 1, 2019). [CHED 303]
==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database, which provides information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically-modified) amino acid and nucleic acid sequences (including siRNA and miRNA). With three million unique users per month at peak, PubChem is ranked as one of the most visited chemistry websites in the world. A substantial number of PubChem users are between ages 18 and 24, who are likely to be undergraduate or graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. In this talk, we will present “PubChem Search”, a new web interface that allows users to quickly find desired chemical information. This interface supports chemical name search as well as various types of chemical structure search, including identity/similarity search, superstructure/substructure search, and molecular search. Using PubChem Search, it is also possible to search for journal articles or patent documents that mention a given chemical. The hits returned from a search can be downloaded to local machines or further refined or analyzed in conjunction with other PubChem tools and services. In this presentation, we will demonstrate how the PubChem Search interface can be used to search beyond google for chemical information of interest.
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.
PubChem: a public chemical information resource for big data chemistrySunghwan Kim
Presented at the Joint Statistical Meetings (JSM) 2020 (virtual) on August 3, 2020.
==== Abstract ====
The idea of “big data” has recently been drawing much attention of the scientific community as well as the general public. An example of big data in Chemistry is the data contained in PubChem, which is a public database of chemical substance descriptions and their biological activities at the National Institutes of Health. PubChem is a sizeable system with 235 million depositor-provided substance descriptions, 96 million unique chemical structures, 1.1 million biological assays, and 268 million biological activity result outcomes. It also contains significant amounts of scientific research data and the inter-relationships between chemicals, proteins, genes, scientific literature, patents and more. PubChem resources have been used in many studies for developing bioactivity and toxicity prediction models, discovering multi-target ligands, and identifying new macromolecule targets of compounds (for drug-repurposing or off-target side effect prediction). This presentation provides an overview of how PubChem’s data, tools, and services can be used for bioassay data analysis and virtual screening (VS) and discusses important aspects of exploiting PubChem for drug discovery.
The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
Learn how to search VHL Search Portal:
- How to start a search?
- What is the methodology for an efficient search? (search question, define database, descriptors, identify keywords, search the databases);
- Check the standard search terms on DeCS;
- Checking the standard terms, search on VHL.
Learn how to identify what to look for when selecting resources; judge if information will be relevant for your assignments and recognise if a source is credible.
This presentation shares a 10 minute pitch of big data potentials in the field of life sciences as presented at the 2015 CMS Global Life Science Forum on Nov 9, 2015 in Frankfurt
A Guided Tour of Issues and Trends (The 13th Annual Health Sciences Lively Lu...Charleston Conference
Ramune K Kubilius (speaker), Andrea Twiss-Brooks (speaker), Anneliese Taylor (speaker), Deborah Blecic (speaker), Elizabeth Ketterman (speaker), Marysue Schaffer (speaker), Robin Champieux (speaker)
BioSHaRE Catalogue of tools and services for data sharingLisette Giepmans
BioSHaRE has developed tools and methods for
i) Data description, presentation and search;
ii) Data harmonisation across databases;
iii) Data analysis across databases;
iv) Contributor recognition;
v) Standardisation of sample handling; and
vi) Ethical, Legal and Social Implications (ELSI).
Download our catalogue for a complete overview of these tools and methods, including how they can be applied, target users, status and accessibility, requirements for usage, and any relevant publications or reference materials.
This catalogue offers a complete overview of these tools and methods, including how they can be applied, target users, status and accessibility, requirements for usage, and any relevant publications or reference materials.
The BioSHaRE approach for epidemiological research across multiple biobanks is described in detail and illustrated by two scientific projects. Furthermore, ‘key’ services are described that are provided by BioSHaRE partners for policy interoperability and data access (link), data harmonisation and federated analyses (link) which are integral to the BioSHaRE approach.
Sitations are the way that researchers communicate how
their work builds on and relates to the work of others and
they can be used to trace how a discovery spreads and is
used by researchers in different disciplines and countries.
Creating a truly comprehensive map of scholarship,
however, relies on having a curated machine-readable
database of citation information, where the provenance of
every citation is clear and reusable. The Initiative for Open
Citations (I4OC), a campaign launched on 6 April 2017,
sought to make publisher members of Crossref aware that
they could open up the citation metadata they already give
to Crossref simply by asking them. With the support of
major publishers and the endorsement of funders and other
organisations, more than 50% of citation data in Crossref
is now freely available, up from less than 1% before the
campaign. This provides the foundation of a well-structured,
open database of literally millions of datapoints that anyone
can query, mine, consume and explore. The presenter will
discuss the aims of the campaign, the new innovative
services that are already using the data, what more still
needs to be done and how you can support the initiative.
Catriona J MacCallum, Hindawi
Presentation on various developments in rapid reviews, inlcuding Cochrane Response and TRIP Rapid Reviews.
Presented at WEB&Z meeting (Dutch medical information specilists) November 28, 2013
Access Lab 2020: Context aware unified institutional knowledge services: an open architecture for digital libraries to offer a seamless user journey to content
Alvet Miranda, senior manager or South/West Asia, Oceania and Africa, EBSCO
Similar to Natalya Csatari_Library Database and Website Search (20)
3. LIBRARY DATABASE AND WEBSITE 3
Abstract
Hospital-acquired infections are a serious issue in hospitals and medical facilities in the United
States, as they not only impair the health outcomes of hospitalized patients, but also cost the
medical and healthcare industries millions of additional dollars to treat. This means that these
types of infections can seriously compromise the health status of patients and force health
facilities to allocate additional resources to the care of these patients. As a result, it is critical that
hospitals implement specific guidelines, policies, and protocols for staff to follow in order to
reduce the risk that patients will acquire and contract these types of infections. These protocols
include rigorous and regular hand washing and the disinfection of commonly touched surfaces in
these facilities that both nurses and patients can come in contact with. These types of policies, if
properly followed by staff, can significantly reduce the risk of the transmission of hospital-
acquired infections to patients during their hospitalization.
Key Words: hospital-acquired infections, hospitalizations, health effects, health outcomes,
policies, prevention
Library Database and Website Search
Hospital-acquired infections are a serious issue in healthcare. Research has shown that
the longer that patients stay in the hospital, the higher is their risk of contracting a hospital
acquired infection (Wolkewitz et al., 2016). Beyond this, the risk of infections can also increase
if external factors, such as the number of infections increasing increasing regardless of the
precautions taken to control them, are found to be a contributing variable (Wolkewitz et al.,
2016).
4. LIBRARY DATABASE AND WEBSITE 4
WWW Search
The Word Wide Web Search was helpful in terms of obtaining a general idea of what this
particular topic of interest is all about. The search generated multiple results from a variety of
websites. Some of these websites were more credible and reliable in nature, such as
governmental websites, while others were less reliable in that they were published in blog
format, which meant that they were not peer reviewed and may not have included the use of
credible sources. Google was the search engine that was used for this assignment. A screenshot
of the WWW search is included in Appendix A and B.
When the general term of hospital-acquired infections was used in the Google search, it
produced over 8.7 million results. This greatly advanced the search, since it produced multiple
results and provided an overview of some of the issues that would be related to this particular
topic. The results of this search can be seen in Appendix A. This topic was further restricted by
putting the search terms of hospital acquired infections in quotation marks, which reduced the
results to 475,000 results. The results of this search can be seen in Appendix B.
The first website source that was evaluated was the Centers for Disease Control and
Prevention. A screenshot of this website can be seen in Appendix C. Based on the criteria
published by Kent, the website is credible, as it is a governmental website and uses research in
order to base its findings on. The website is also objective, as the information that is found here
is not biased. The website was last updated on May 27, 2016, which means that it is current.
CDC also includes many sources in the articles that it publishes, which means that it is accurate.
Finally, this source is usable, as as the content is organized and users can easily and quickly find
what they are looking for. The second website that was assessed was Medscape. This website
also met all the criteria based on Cornell’s University Library. The website is accurate, and
authoritative, as it reviewed by medical professionals.
5. LIBRARY DATABASE AND WEBSITE 5
Database Search
The database search was helpful in terms of locating credible peer-reviewed sources that
were supported by relevant research and literature. The two databases that were utilized for this
assignment were CINAHL and Business Source Complete. Both of these databases allow users
to customize their searchers through either basic or advance options. CINAHL generated
multiple results, while Business Source Complete only generated a handful of sources that could
be, potentially, useful. The WWW search differed from the MU library search techniques in that
it does not allow users to specify that they only want to use peer-reviewed sources. Additionally,
the WWW search does not allow users to restrict their search to specific time frames or to
publications in specific languages or which are published in specific journals. The search was
limited and advanced through the use of specific key words, delimiters, such as “and” and “or,”
restricting the results to only peer reviewed sources, and restricting the time frame of the
publication to only specific years or ranges of years. These options allow users to generate fewer
results that are much more specific to their search.
The article written by Fox et al. (2015) discusses how hand washing by nurses can
significantly decrease the number of hospital acquired infections that hospitalized patients can
contract. According to the authors of this article, about 2.5 million infections are transmitted
between patients and between nurses and patients in the United States every single year (Fox et
al., 2015). This has contributed to costs of more than $4.5 billion every single year that
Table 1 Comparison of Database Search using Advance and Limited Searches
Library Data Base Search Options
CINAHL Business Source
Complete
Topic/
Key words
Search Results Peer Review
Articles
Full Text
Articles
Dates
limited to
2010-2016
Age
65+
X Hospital acquired
infections
1,207 1.034 344 566 --
X Hospital acquired
infections
5 5 5 5 --
6. LIBRARY DATABASE AND WEBSITE 6
healthcare facilities in the U.S. have to account for (Fox et al., 2015). However, a policy of hand
washing can reduce these costs by about $40,000 with every single infection that is avoided and,
overall, reduce the incidence of these infections by up to 30% (Fox et al., 2015).
The article written by Taylor and Shekerdemian (2016) is not published in the data in full
text format. However, the article could be obtained through the MU library loaning it from one
of its affiliated libraries. In addition to this, this article could also be obtained through the library
requesting a copy of this article from the publisher.
7. LIBRARY DATABASE AND WEBSITE 7
References
CDC. (2016). Healthcare-associated infections (HAI). Centers for Disease Control and
Prevention. Retrieved from http://www.cdc.gov/HAi/
Custodio, H. T. (2014, September 16). Hospital-acquired infections. Medscape. Retrieved from
http://emedicine.medscape.com/article/967022-
overview?pa=4YTeiMDLhVAsUlTVpr200kyJc9wMDBrYugzmhJC8refxZDOkqtOurc
W5dggiTE51z96uGsTAci76hIk%2FxX6YTbOwhd8Mdk7tVO%2FdkscsGC4%3D
Fox, C., Wavra, T., Ash Drake, D., Mulligan, D., Pacheco Bennett, Y., Nelson, C., Kirkwood, P.,
Jones, L., & Bader, M. K. (2015). Use of a patient hand hygiene protocol to reduce
hospital-acquired infections and improve nurses’ hand washing. American Journal of
Critical Care, 24(3), 216-224.
Olsen, M. A., Young-Xu, Y., Stwalley, D., Kelly, C. P., Gerding, D. N., Saeed, M. J., Mahe, C.,
& Dubberke, E. R. (2016). The burden of clostridium difficile infection: Estimates of the
incidence of CDI from U.S. administrative databases. BMC Infectious Diseases, 16, 1-8.
Taylor, R. S., & Shekerdemian, L. S. (20160. Avoidance of hospital-acquired infections in
pediatric cardiac surgical patients. Pediatric Critical Care Medicine, 17, 279-286.
Wolkewitz, M., Cooper, B. S., Palomar-Martinez, M., Alvarez-Lerma, F., Olaechea-Astigarraga,
P., Barnett, A. G., & Schumacher, M. (2016). Multiple time scales in modeling the
incidence of infections acquired in intensive care units. BMC Medical Research
Methodology, 16, 1-11.