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https://www.readbyqxmd.com/read/27899649/protein-ontology-pro-enhancing-and-scaling-up-the-representation-of-protein-entities
#1
Darren A Natale, Cecilia N Arighi, Judith A Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R Christie, Julie Cowart, Peter D'Eustachio, Alexander D Diehl, Harold J Drabkin, William D Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H Wu
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27846332/purls-monitoring-home-bp-readings-just-got-easier
#2
Jennie B Jarrett, Linda Hogan, Corey Lyon, Kate Rowland
This novel method of identifying patients with uncontrolled hypertension correlates well with ambulatory BP monitoring.
October 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27818108/gating-role-of-his-72-in-tmpurl-enzyme-uncovered-by-structural-analyses-and-molecular-dynamics-simulations
#3
Biplab Ghosh, Venuka Durani Goyal
Histidine is ubiquitous in enzyme active sites but its role is often difficult to ascribe due to ambiguity of protonation state and complex electrostatic and dynamic effects involved. In this study the role of His 72 in TmPurL, a glutamine amidotransferase (GAT) enzyme, is investigated. TmPurL is a large 66kDa enzyme that works as part of an even larger (>100kDa) multi-protein complex. This enzyme complex performs an essential step in the purine biosynthesis pathway by abstracting ammonia from a glutamine molecule and channeling it 30Å away into the active site of TmPurL, incorporating it into a purine biosynthesis intermediate...
October 25, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27672689/purls-yeast-infection-in-pregnancy-think-twice-about-fluconazole
#4
Amir Barzin, Anne Mounsey
This study's findings regarding the risk of miscarriage may mean it's time to forego fluconazole in favor of topical azoles as first-line treatment.
September 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27664130/the-environment-ontology-in-2016-bridging-domains-with-increased-scope-semantic-density-and-interoperation
#5
Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E Lewis, Mark P Schildhauer, Ramona L Walls, Christopher J Mungall
BACKGROUND: The Environment Ontology (ENVO; http://www.environmentontology.org/ ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description...
September 23, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27660840/purls-on-demand-pill-protocol-protects-against-hiv
#6
Kathryn Justesen, Shailendra Prasad
Finally, there's an effective prevention strategy--other than condoms--that can be used, as needed, by patients at high risk for HIV infection.
August 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27565102/purls-light-therapy-for-nonseasonal-major-depressive-disorder
#7
Kehinde Eniola, Angela Bacigalupo, Anne Mounsey
While bright light therapy already has a place in the treatment of seasonal affective disorder, a recent trial spotlights its utility beyond the winter months.
July 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27538448/the-apollo-structured-vocabulary-an-owl2-ontology-of-phenomena-in-infectious-disease-epidemiology-and-population-biology-for-use-in-epidemic-simulation
#8
William R Hogan, Michael M Wagner, Mathias Brochhausen, John Levander, Shawn T Brown, Nicholas Millett, Jay DePasse, Josh Hanna
BACKGROUND: We developed the Apollo Structured Vocabulary (Apollo-SV)-an OWL2 ontology of phenomena in infectious disease epidemiology and population biology-as part of a project whose goal is to increase the use of epidemic simulators in public health practice. Apollo-SV defines a terminology for use in simulator configuration. Apollo-SV is the product of an ontological analysis of the domain of infectious disease epidemiology, with particular attention to the inputs and outputs of nine simulators...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27487927/crystal-structures-of-a-subunit-of-the-formylglycinamide-ribonucleotide-amidotransferase-purs-from-thermus-thermophilus-sulfolobus-tokodaii-and-methanocaldococcus-jannaschii
#9
Yuzo Watanabe, Hisaaki Yanai, Mayumi Kanagawa, Sakiko Suzuki, Satoko Tamura, Kiyoshi Okada, Seiki Baba, Takashi Kumasaka, Yoshihiro Agari, Lirong Chen, Zheng Qing Fu, John Chrzas, Bi Cheng Wang, Noriko Nakagawa, Akio Ebihara, Ryoji Masui, Seiki Kuramitsu, Shigeyuki Yokoyama, Gen Ichi Sampei, Gota Kawai
The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date...
August 2016: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/27474822/purls-more-isn-t-better-with-acute-low-back-pain-treatment
#10
Kevin Frazer, James J Stevermer
Adding cyclobenzaprine or oxycodone/acetaminophen to naproxen for the treatment of acute low back pain does nothing more than increase adverse effects.
June 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27275941/a-valuable-string-of-purls
#11
EDITORIAL
John Hickner
To qualify as a PURL, a study had to meet 6 criteria. It had to be scientifically valid, relevant to family medicine, applicable in a medical care setting, immediately implementable, clinically meaningful, and practice changing. These criteria still stand today.
May 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27275938/purls-go-low-or-say-no-to-aggressive-systolic-bp-goals
#12
REVIEW
Margaret Day, James J Stevermer
The SPRINT trial demonstrated the benefits--and risks--of reaching a systolic target <120 mm Hg in non-diabetic patients at high risk for CV events. Here's who might benefit.
May 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27262250/purls-resistant-hypertension-time-to-consider-this-fourth-line-drug
#13
Alexander Kaysin, Anne Mounsey
For most adults with resistant hypertension, spironolactone is superior to doxazosin and bisoprolol as an adjunct to triple therapy.
April 2016: Journal of Family Practice
https://www.readbyqxmd.com/read/27259657/the-orthology-ontology-development-and-applications
#14
Jesualdo Tomás Fernández-Breis, Hirokazu Chiba, María Del Carmen Legaz-García, Ikuo Uchiyama
BACKGROUND: Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides establishing evolutionary relations among genes of organisms and allows functional inference of gene products. However, the wide variations in current orthology databases necessitate the research toward the shareability of the content that is generated by different tools and stored in different structures...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27235801/from-frames-to-owl2-converting-the-foundational-model-of-anatomy
#15
Landon T Detwiler, Jose L V Mejino, James F Brinkley
OBJECTIVE: The Foundational Model of Anatomy (FMA) [Rosse C, Mejino JLV. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36:478-500] is an ontology that represents canonical anatomy at levels ranging from the entire body to biological macromolecules, and has rapidly become the primary reference ontology for human anatomy, and a template for model organisms. Prior to this work, the FMA was developed in a knowledge modeling language known as Protégé Frames...
May 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27175225/omnisearch-a-semantic-search-system-based-on-the-ontology-for-microrna-target-omit-for-microrna-target-gene-interaction-data
#16
Jingshan Huang, Fernando Gutierrez, Harrison J Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A Blake, Karen Eilbeck, Darren A Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M Borchert, Ming Tan, Alan Ruttenberg
As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27152146/the-non-coding-rna-ontology-ncro-a-comprehensive-resource-for-the-unification-of-non-coding-rna-biology
#17
Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A Blake, Dejing Dou, Weili Huang, Darren A Natale, Alan Ruttenberg, Jun Huan, Michael T Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M Borchert, Ming Tan
In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27148435/obib-a-novel-ontology-for-biobanking
#18
Mathias Brochhausen, Jie Zheng, David Birtwell, Heather Williams, Anna Maria Masci, Helena Judge Ellis, Christian J Stoeckert
BACKGROUND: Biobanking necessitates extensive integration of data to allow data analysis and specimen sharing. Ontologies have been demonstrated to be a promising approach in fostering better semantic integration of biobank-related data. Hitherto no ontology provided the coverage needed to capture a broad spectrum of biobank user scenarios. METHODS: Based in the principles laid out by the Open Biological and Biomedical Ontologies Foundry two biobanking ontologies have been developed...
2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27128319/the-ontology-for-biomedical-investigations
#19
Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H Brush, Bill Bug, Marcus C Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Daniel Schober, Barry Smith, Larisa N Soldatova, Christian J Stoeckert, Chris F Taylor, Carlo Torniai, Jessica A Turner, Randi Vita, Patricia L Whetzel, Jie Zheng
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources...
2016: PloS One
https://www.readbyqxmd.com/read/27096073/an-accurate-and-precise-representation-of-drug-ingredients
#20
Josh Hanna, Jiang Bian, William R Hogan
BACKGROUND: In previous work, we built the Drug Ontology (DrOn) to support comparative effectiveness research use cases. Here, we have updated our representation of ingredients to include both active ingredients (and their strengths) and excipients. Our update had three primary lines of work: 1) analysing and extracting excipients, 2) analysing and extracting strength information for active ingredients, and 3) representing the binding of active ingredients to cytochrome P450 isoenzymes as substrates and inhibitors of those enzymes...
2016: Journal of Biomedical Semantics
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