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Emergency department management of pediatric acute asthma: an evidence-based review
Zelicof Paul, Audrey; Rutherford, Kim A; Abuso, Stephanie M
Asthma is the most common chronic disease of childhood. Although home action plans and the use of maintenance medications have improved daily management and control of asthma, many children still require emergency department care at least once per year. Emergency clinicians must be able to manage patients with acute asthma exacerbations and determine their safe disposition. This issue reviews the current evidence-based emergency department management recommendations for moderate to severe acute asthma in pediatric patients. Timely use of bronchodilators and systemic corticosteroids, as well as adjunct modalities, are discussed. Current challenges in asthma management related to vaping and COVID-19 are also addressed.
PMID: 37352408
ISSN: 1549-9669
CID: 5539952
The Gene Ontology knowledgebase in 2023
,; Aleksander, Suzi A; Balhoff, James; Carbon, Seth; Cherry, J Michael; Drabkin, Harold J; Ebert, Dustin; Feuermann, Marc; Gaudet, Pascale; Harris, Nomi L; Hill, David P; Lee, Raymond; Mi, Huaiyu; Moxon, Sierra; Mungall, Christopher J; Muruganugan, Anushya; Mushayahama, Tremayne; Sternberg, Paul W; Thomas, Paul D; Van Auken, Kimberly; Ramsey, Jolene; Siegele, Deborah A; Chisholm, Rex L; Fey, Petra; Aspromonte, Maria Cristina; Nugnes, Maria Victoria; Quaglia, Federica; Tosatto, Silvio; Giglio, Michelle; Nadendla, Suvarna; Antonazzo, Giulia; Attrill, Helen; Dos Santos, Gil; Marygold, Steven; Strelets, Victor; Tabone, Christopher J; Thurmond, Jim; Zhou, Pinglei; Ahmed, Saadullah H; Asanitthong, Praoparn; Luna Buitrago, Diana; Erdol, Meltem N; Gage, Matthew C; Ali Kadhum, Mohamed; Li, Kan Yan Chloe; Long, Miao; Michalak, Aleksandra; Pesala, Angeline; Pritazahra, Armalya; Saverimuttu, Shirin C C; Su, Renzhi; Thurlow, Kate E; Lovering, Ruth C; Logie, Colin; Oliferenko, Snezhana; Blake, Judith; Christie, Karen; Corbani, Lori; Dolan, Mary E; Drabkin, Harold J; Hill, David P; Ni, Li; Sitnikov, Dmitry; Smith, Cynthia; Cuzick, Alayne; Seager, James; Cooper, Laurel; Elser, Justin; Jaiswal, Pankaj; Gupta, Parul; Jaiswal, Pankaj; Naithani, Sushma; Lera-Ramirez, Manuel; Rutherford, Kim; Wood, Valerie; De Pons, Jeffrey L; Dwinell, Melinda R; Hayman, G Thomas; Kaldunski, Mary L; Kwitek, Anne E; Laulederkind, Stanley J F; Tutaj, Marek A; Vedi, Mahima; Wang, Shur-Jen; D'Eustachio, Peter; Aimo, Lucila; Axelsen, Kristian; Bridge, Alan; Hyka-Nouspikel, Nevila; Morgat, Anne; Aleksander, Suzi A; Cherry, J Michael; Engel, Stacia R; Karra, Kalpana; Miyasato, Stuart R; Nash, Robert S; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Bakker, Erika; Berardini, Tanya Z; Reiser, Leonore; Auchincloss, Andrea; Axelsen, Kristian; Argoud-Puy, Ghislaine; Blatter, Marie-Claude; Boutet, Emmanuel; Breuza, Lionel; Bridge, Alan; Casals-Casas, Cristina; Coudert, Elisabeth; Estreicher, Anne; Livia Famiglietti, Maria; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hulo, Chantal; Hyka-Nouspikel, Nevila; Jungo, Florence; Le Mercier, Philippe; Lieberherr, Damien; Masson, Patrick; Morgat, Anne; Pedruzzi, Ivo; Pourcel, Lucille; Poux, Sylvain; Rivoire, Catherine; Sundaram, Shyamala; Bateman, Alex; Bowler-Barnett, Emily; Bye-A-Jee, Hema; Denny, Paul; Ignatchenko, Alexandr; Ishtiaq, Rizwan; Lock, Antonia; Lussi, Yvonne; Magrane, Michele; Martin, Maria J; Orchard, Sandra; Raposo, Pedro; Speretta, Elena; Tyagi, Nidhi; Warner, Kate; Zaru, Rossana; Diehl, Alexander D; Lee, Raymond; Chan, Juancarlos; Diamantakis, Stavros; Raciti, Daniela; Zarowiecki, Magdalena; Fisher, Malcolm; James-Zorn, Christina; Ponferrada, Virgilio; Zorn, Aaron; Ramachandran, Sridhar; Ruzicka, Leyla; Westerfield, Monte
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.
PMCID:10158837
PMID: 36866529
ISSN: 1943-2631
CID: 5609782
The Gene Ontology resource: enriching a GOld mine
Carbon, Seth; Douglass, Eric; Good, Benjamin M.; Unni, Deepak R.; Harris, Nomi L.; Mungall, Christopher J.; Basu, Siddartha; Chisholm, Rex L.; Dodson, Robert J.; Hartline, Eric; Fey, Petra; Thomas, Paul D.; Albou, Laurent-Philippe; Ebert, Dustin; Kesling, Michael J.; Mi, Huaiyu; Muruganujan, Anushya; Huang, Xiaosong; Mushayahama, Tremayne; LaBonte, Sandra A.; Siegele, Deborah A.; Antonazzo, Giulia; Attrill, Helen; Brown, Nick H.; Garapati, Phani; Marygold, Steven J.; Trovisco, Vitor; Dos Santos, Gil; Falls, Kathleen; Tabone, Christopher; Zhou, Pinglei; Goodman, Joshua L.; Strelets, Victor B.; Thurmond, Jim; Garmiri, Penelope; Ishtiaq, Rizwan; Rodriguez-Lopez, Milagros; Acencio, Marcio L.; Kuiper, Martin; Laegreid, Astrid; Logie, Colin; Lovering, Ruth C.; Kramarz, Barbara; Saverimuttu, Shirin C. C.; Pinheiro, Sandra M.; Gunn, Heather; Su, Renzhi; Thurlow, Katherine E.; Chibucos, Marcus; Giglio, Michelle; Nadendla, Suvarna; Munro, James; Jackson, Rebecca; Duesbury, Margaret J.; Del-Toro, Noemi; Meldal, Birgit H. M.; Paneerselvam, Kalpana; Perfetto, Livia; Porras, Pablo; Orchard, Sandra; Shrivastava, Anjali; Chang, Hsin-Yu; Finn, Robert Daniel; Mitchell, Alexander Lawson; Rawlings, Neil David; Richardson, Lorna; Sangrador-Vegas, Amaia; Blake, Judith A.; Christie, Karen R.; Dolan, Mary E.; Drabkin, Harold J.; Hill, David P.; Ni, Li; Sitnikov, Dmitry M.; Harris, Midori A.; Oliver, Stephen G.; Rutherford, Kim; Wood, Valerie; Hayles, Jaqueline; Bahler, Jurg; Bolton, Elizabeth R.; De Pons, Jeffery L.; Dwinell, Melinda R.; Hayman, G. Thomas; Kaldunski, Mary L.; Kwitek, Anne E.; Laulederkind, Stanley J. F.; Plasterer, Cody; Tutaj, Marek A.; Vedi, Mahima; Wang, Shur-Jen; D\Eustachio, Peter; Matthews, Lisa; Balhoff, James P.; Aleksander, Suzi A.; Alexander, Michael J.; Cherry, J. Michael; Engel, Stacia R.; Gondwe, Felix; Karra, Kalpana; Miyasato, Stuart R.; Nash, Robert S.; Simison, Matt; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Feuermann, Marc; Gaudet, Pascale; Morgat, Anne; Bakker, Erica; Berardini, Tanya Z.; Reiser, Leonore; Subramaniam, Shabari; Huala, Eva; Arighi, Cecilia N.; Auchincloss, Andrea; Axelsen, Kristian; Argoud-Puy, Ghislaine; Bateman, Alex; Blatter, Marie-Claude; Boutet, Emmanuel; Bowler, Emily; Breuza, Lionel; Bridge, Alan; Britto, Ramona; Bye-A-Jee, Hema; Casas, Cristina Casals; Coudert, Elisabeth; Denny, Paul; Estreicher, Anne; Famiglietti, Maria Livia; Georghiou, George; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hatton-Ellis, Emma; Hulo, Chantal; Ignatchenko, Alexandr; Jungo, Florence; Laiho, Kati; Le Mercier, Philippe; Lieberherr, Damien; Lock, Antonia; Lussi, Yvonne; MacDougall, Alistair; Magrane, Michele; Martin, Maria J.; Masson, Patrick; Natale, Darren A.; Hyka-Nouspikel, Nevila; Orchard, Sandra; Pedruzzi, Ivo; Pourcel, Lucille; Poux, Sylvain; Pundir, Sangya; Rivoire, Catherine; Speretta, Elena; Sundaram, Shyamala; Tyagi, Nidhi; Warner, Kate; Zaru, Rossana; Wu, Cathy H.; Diehl, Alexander D.; Chan, Juancarlos N.; Grove, Christian; Lee, Raymond Y. N.; Muller, Hans-Michael; Raciti, Daniela; Van Auken, Kimberly; Sternberg, Paul W.; Berriman, Matthew; Paulini, Michael; Howe, Kevin; Gao, Sibyl; Wright, Adam; Stein, Lincoln; Howe, Douglas G.; Toro, Sabrina; Westerfield, Monte; Jaiswal, Pankaj; Cooper, Laurel; Elser, Justin
ISI:000608437800042
ISSN: 0305-1048
CID: 4774022
The Gene Ontology Resource: 20 years and still GOing strong
Carbon, S; Douglass, E; Dunn, N; Good, B; Harris, N L; Lewis, S E; Mungall, C J; Basu, S; Chisholm, R L; Dodson, R J; Hartline, E; Fey, P; Thomas, P D; Albou, L P; Ebert, D; Kesling, M J; Mi, H; Muruganujan, A; Huang, X; Poudel, S; Mushayahama, T; Hu, J C; LaBonte, S A; Siegele, D A; Antonazzo, G; Attrill, H; Brown, N H; Fexova, S; Garapati, P; Jones, T E M; Marygold, S J; Millburn, G H; Rey, A J; Trovisco, V; Dos, Santos G; Emmert, D B; Falls, K; Zhou, P; Goodman, J L; Strelets, V B; Thurmond, J; Courtot, M; Osumi, D -S; Parkinson, H; Roncaglia, P; Acencio, M L; Kuiper, M; Lreid, A; Logie, C; Lovering, R C; Huntley, R P; Denny, P; Campbell, N H; Kramarz, B; Acquaah, V; Ahmad, S H; Chen, H; Rawson, J H; Chibucos, M C; Giglio, M; Nadendla, S; Tauber, R; Duesbury, M J; Del, N -T; Meldal, B H M; Perfetto, L; Porras, P; Orchard, S; Shrivastava, A; Xie, Z; Chang, H Y; Finn, R D; Mitchell, A L; Rawlings, N D; Richardson, L; Sangrador-Vegas, A; Blake, J A; Christie, K R; Dolan, M E; Drabkin, H J; Hill, D P; Ni, L; Sitnikov, D; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Hayles, J; Bahler, J; Lock, A; Bolton, E R; De, Pons J; Dwinell, M; Hayman, G T; Laulederkind, S J F; Shimoyama, M; Tutaj, M; Wang, S -J; D'Eustachio, P; Matthews, L; Balhoff, J P; Aleksander, S A; Binkley, G; Dunn, B L; Cherry, J M; Engel, S R; Gondwe, F; Karra, K; MacPherson, K A; Miyasato, S R; Nash, R S; Ng, P C; Sheppard, T K; Shrivatsav, Vp A; Simison, M; Skrzypek, M S; Weng, S; Wong, E D; Feuermann, M; Gaudet, P; Bakker, E; Berardini, T Z; Reiser, L; Subramaniam, S; Huala, E; Arighi, C; Auchincloss, A; Axelsen, K; Argoud, G -P; Bateman, A; Bely, B; Blatter, M -C; Boutet, E; Breuza, L; Bridge, A; Britto, R; Bye-A-Jee, H; Casals-Casas, C; Coudert, E; Estreicher, A; Famiglietti, L; Garmiri, P; Georghiou, G; Gos, A; Gruaz-Gumowski, N; Hatton-Ellis, E; Hinz, U; Hulo, C; Ignatchenko, A; Jungo, F; Keller, G; Laiho, K; Lemercier, P; Lieberherr, D; Lussi, Y; Mac-Dougall, A; Magrane, M; Martin, M J; Masson, P; Natale, D A; Hyka, N -N; Pedruzzi, I; Pichler, K; Poux, S; Rivoire, C; Rodriguez-Lopez, M; Sawford, T; Speretta, E; Shypitsyna, A; Stutz, A; Sundaram, S; Tognolli, M; Tyagi, N; Warner, K; Zaru, R; Wu, C; Chan, J; Cho, J; Gao, S; Grove, C; Harrison, M C; Howe, K; Lee, R; Mendel, J; Muller, H -M; Raciti, D; Van, Auken K; Berriman, M; Stein, L; Sternberg, P W; Howe, D; Toro, S; Westerfield, M
The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-Throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the a GO ribbon' widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.
EMBASE:626499713
ISSN: 1362-4962
CID: 3788062
Measuring Assessment Quality With an Assessment Utility Rubric for Medical Education
Colbert-Getz, Jorie M; Ryan, Michael; Hennessey, Erin; Lindeman, Brenessa; Pitts, Brian; Rutherford, Kim A; Schwengel, Deborah; Sozio, Stephen M; George, Jessica; Jung, Julianna
Introduction/UNASSIGNED:Prior research has identified seven elements of a good assessment, but the elements have not been operationalized in the form of a rubric to rate assessment utility. It would be valuable for medical educators to have a systematic way to evaluate the utility of an assessment in order to determine if the assessment used is optimal for the setting. Methods/UNASSIGNED:We developed and refined an assessment utility rubric using a modified Delphi process. Twenty-nine graduate students pilot-tested the rubric in 2016 with hypothetical data from three examinations, and interrater reliability of rubric scores was measured with interclass correlation coefficients (ICCs). Results/UNASSIGNED:Consensus for all rubric items was reached after three rounds. The resulting assessment utility rubric includes four elements (equivalence, educational effect, catalytic effect, acceptability) with three items each, one element (validity evidence) with five items, and space to provide four feasibility items relating to time and cost. Rater scores had ICC values greater than .75. Discussion/UNASSIGNED:The rubric shows promise in allowing educators to evaluate the utility of an assessment specific to their setting. The medical education field needs to give more consideration to how an assessment drives learning forward, how it motivates trainees, and whether it produces acceptable ranges of scores for all stakeholders.
PMCID:6338154
PMID: 30800790
ISSN: 2374-8265
CID: 3721652
Expansion of the gene ontology knowledgebase and resources: The gene ontology consortium
Carbon, S; Dietze, H; Lewis, S E; Mungall, C J; Munoz-Torres, M C; Basu, S; Chisholm, R L; Dodson, R J; Fey, P; Thomas, P D; Mi, H; Muruganujan, A; Huang, X; Poudel, S; Hu, J C; Aleksander, S A; McIntosh, B K; Renfro, D P; Siegele, D A; Antonazzo, G; Attrill, H; Brown, N H; Marygold, S J; Mc-Quilton, P; Ponting, L; Millburn, G H; Rey, A J; Stefancsik, R; Tweedie, S; Falls, K; Schroeder, A J; Courtot, M; Osumi-Sutherland, D; Parkinson, H; Roncaglia, P; Lovering, R C; Foulger, R E; Huntley, R P; Denny, P; Campbell, N H; Kramarz, B; Patel, S; Buxton, J L; Umrao, Z; Deng, A T; Alrohaif, H; Mitchell, K; Ratnaraj, F; Omer, W; Rodriguez-Lopez, M; C , Chibucos M; Giglio, M; Nadendla, S; Duesbury, M J; Koch, M; Meldal, B H M; Melidoni, A; Porras, P; Orchard, S; Shrivastava, A; Chang, H Y; Finn, R D; Fraser, M; Mitchell, A L; Nuka, G; Potter, S; Rawlings, N D; Richardson, L; Sangrador-Vegas, A; Young, S Y; Blake, J A; Christie, K R; Dolan, M E; Drabkin, H J; Hill, D P; Ni, L; Sitnikov, D; Harris, M A; Hayles, J; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; De, Pons J; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, G T; Tutaj, M; Wang, S -J; D'Eustachio, P; Matthews, L; Balhoff, J P; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Engel, S R; Miyasato, S R; Nash, R S; Simison, M; Skrzypek, M S; Weng, S; Wong, E D; Feuermann, M; Gaudet, P; Berardini, T Z; Li, D; Muller, B; Reiser, L; Huala, E; Argasinska, J; Arighi, C; Auchincloss, A; Axelsen, K; Argoud-Puy, G; Bateman, A; Bely, B; Blatter, M -C; Bonilla, C; Bougueleret, L; Boutet, E; Breuza, L; Bridge, A; Britto, R; Hye-, A-Bye H; Casals, C; Cibrian-Uhalte, E; Coudert, E; Cusin, I; Duek-Roggli, P; Estreicher, A; Famiglietti, L; Gane, P; Garmiri, P; Georghiou, G; Gos, A; Gruaz-Gumowski, N; Hatton-Ellis, E; Hinz, U; Holmes, A; Hulo, C; Jungo, F; Keller, G; Laiho, K; Lemercier, P; Lieberherr, D; Mac-, Dougall A; Magrane, M; Martin, M J; Masson, P; Natale, D A; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Speretta, E; Shypitsyna, A; Stutz, A; Sundaram, S; Tognolli, M; Wu, C; Xenarios, I; Yeh, L -S; Chan, J; Gao, S; Howe, K; Kishore, R; Lee, R; Li, Y; Lomax, J; Muller, H -M; Raciti, D; Van, Auken K; Berriman, M; Stein,, Paul Kersey L; W , Sternberg P; Howe, D; Westerfield, M
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of-omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit https://urldefense.proofpoint.com/v2/url?u=http- 3A__geneontology.org_&d=DQIBAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=vQfPybH YMptZTsGTKf8YZN_ho- QhkqmSqA9bfoe84p4&m=FWECBidVXo0ALQwQIUv7WM1GHzTeBIhQYi8nAqMZqzw&s=Bbv_JsLtuGTdO OEXNgUM5nbQSx8-Zf7uwXSJpJ2Najk&e= .
EMBASE:614949963
ISSN: 0305-1048
CID: 2685722
Gene Ontology Consortium: going forward
Blake, JA; Christie, KR; Dolan, ME; Drabkin, HJ; Hill, DP; Ni, L; Sitnikov, D; Burgess, S; Buza, T; Gresham, C; McCarthy, F; Pillai, L; Wang, H; Carbon, S; Dietze, H; Lewis, SE; Mungall, CJ; Munoz-Torres, MC; Feuermann, M; Gaudet, P; Basu, S; Chisholm, RL; Dodson, RJ; Fey, P; Mi, H; Thomas, PD; Muruganujan, A; Poudel, S; Hu, JC; Aleksander, SA; McIntosh, BK; Renfro, DP; Siegele, DA; Attrill, H; Brown, NH; Tweedie, S; Lomax, J; Osumi-Sutherland, D; Parkinson, H; Roncaglia, P; Lovering, RC; Talmud, PJ; Humphries, SE; Denny, P; Campbell, NH; Foulger, RE; Chibucos, MC; Giglio, MGwinn; Chang, HY; Finn, R; Fraser, M; Mitchell, A; Nuka, G; Pesseat, S; Sangrador, A; Scheremetjew, M; Young, SY; Stephan, R; Harris, MA; Oliver, SG; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, PJ; McDowall, MD; Staines, DM; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, GT; Wang, SJ; Petri, V; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, JM; Costanzo, MC; Demeter, J; Dwight, SS; Engel, SR; Hitz, BC; Inglis, DO; Lloyd, P; Miyasato, SR; Paskov, K; Roe, G; Simison, M; Nash, RS; Skrzypek, MS; Weng, S; Wong, ED; Berardini, TZ; Li, D; Huala, E; Argasinska, J; Arighi, C; Auchincloss, A; Axelsen, K; Argoud-Puy, G; Bateman, A; Bely, B; Blatter, MC; Bonilla, C; Bougueleret, L; Boutet, E; Breuza, L; Bridge, A; Britto, R; Casals, C; Cibrian-Uhalte, E; Coudert, E; Cusin, I; Duek-Roggli, P; Estreicher, A; Famiglietti, L; Gane, P; Garmiri, P; Gos, A; Gruaz-Gumowski, N; Hatton-Ellis, E; Hinz, U; Hulo, C; Huntley, R; Jungo, F; Keller, G; Laiho, K; Lemercier, P; Lieberherr, D; MacDougall, A; Magrane, M; Martin, M; Masson, P; Mutowo, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Shypitsyna, A; Stutz, A; Sundaram, S; Tognolli, M; Wu, C; Xenarios, I; Chan, J; Kishore, R; Sternberg, PW; Van Auken, K; Muller, HM; Done, J; Li, Y; Howe, D; Westerfield, M; Gene Ontology Consortium
The Gene Ontology (GO; ext-link-type="uri" xlink:href="http://www.geneontology.org" xlink:type="simple">http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.
ISI:000350210400154
ISSN: 1362-4962
CID: 2337512
Gene Ontology annotations and resources
Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
PMCID:3531070
PMID: 23161678
ISSN: 1362-4962
CID: 2953432
The Gene Ontology: enhancements for 2011
Blake, JA; Dolan, M; Drabkin, H; Hill, DP; Ni, L; Sitnikov, D; Burgess, S; Buza, T; Gresham, C; McCarthy, F; Pillai, L; Wang, H; Carbon, S; Lewis, SE; Mungall, CJ; Gaudet, P; Chisholm, RL; Fey, P; Kibbe, WA; Basu, S; Siegele, DA; McIntosh, BK; Renfro, DP; Zweifel, AE; Hu, JC; Brown, NH; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Argoud-Puy, G; Bely, B; Blatter, M-C; Bougueleret, L; Boutet, E; Branconi-Quintaje, S; Breuza, L; Bridge, A; Browne, P; Chan, WM; Coudert, E; Cusin, I; Dimmer, E; Duek-Roggli, P; Eberhardt, R; Estreicher, A; Famiglietti, L; Ferro-Rojas, S; Feuermann, M; Gardner, M; Gos, A; Gruaz-Gumowski, N; Hinz, U; Hulo, C; Huntley, R; James, J; Jimenez, S; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, MJ; Masson, P; Moinat, M; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Millan, PPorras; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Sehra, H; Stanley, E; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulger, R; Lomax, J; Roncaglia, P; Camon, E; Khodiyar, VK; Lovering, RC; Talmud, PJ; Chibucos, M; Giglio, MGwinn; Dolinski, K; Heinicke, S; Livstone, MS; Stephan, R; Harris, MA; Oliver, SG; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, PJ; McDowall, MD; Staines, DM; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S-J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Amundsen, CD; Balakrishnan, R; Binkley, G; Cherry, JM; Christie, KR; Costanzo, MC; Dwight, SS; Engel, SR; Fisk, DG; Hirschman, JE; Hitz, BC; Hong, EL; Karra, K; Krieger, CJ; Miyasato, SR; Nash, RS; Park, J; Skrzypek, MS; Weng, S; Wong, ED; Berardini, TZ; Li, D; Huala, E; Slonim, D; Wick, H; Thomas, P; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M; Gene Ontology Consortium
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.
ISI:000298601300084
ISSN: 0305-1048
CID: 2337532
Adolescents' perceptions of interpersonal communication, respect, and concern for privacy in an urban tertiary-care pediatric emergency department
Rutherford, Kim A; Pitetti, Raymond D; Zuckerbraun, Noel S; Smola, Susan; Gold, Melanie A
OBJECTIVES: To measure adolescents' perceived overall satisfaction with health care in a pediatric emergency department (PED), identify key factors that contributed to satisfaction, and determine how these factors interacted with length of stay (LOS) and triage acuity. METHODS: Prospective observational design with a convenience sample of 100 adolescents 13 to 21 years old recruited from the PED between February and June 2007. Participants completed a self-administered 27-item written survey with closed and open-ended items. RESULTS: Survey response rate was 99%. Respondents completed the survey in a mean time of 6.6 minutes (range, 3-12 minutes; SD, 2.0 minutes). Most (95%) reported being satisfied with their overall PED experience, and 91% would recommend the PED to other adolescents. Interpersonal communication and respect correlated significantly with respondents' overall satisfaction. There were no statistically significant differences in overall satisfaction rates by sex, age, socioeconomic status, or ethnicity, or by LOS, triage acuity score, or hospital admission. Most (94%) answered a qualitative survey item that asked how their PED care could be improved with 4 distinct responses: no changes necessary, enhance interpersonal communication, improve comfort of stay, and shorten LOS. CONCLUSIONS: Adolescents expressed high levels of satisfaction with their overall PED experience at our institution. Interpersonal communication and respect highly correlated with overall satisfaction. A multicenter study using a similar self-administered survey would further support the relationship between key factors and PED adolescent satisfaction. Utilization of a self-administered survey for adolescent research is feasible in the PED and could be used to improve quality control measures for adolescent care.
PMID: 20401971
ISSN: 1535-1815
CID: 1866422
