J Integr Bioinform - Excemplify: a flexible template based solution, parsing and managing data in spreadsheets for experimentalists.

Tópicos

{ model(2656) set(1616) predict(1553) }
{ method(1219) similar(1157) match(930) }
{ data(1714) softwar(1251) tool(1186) }
{ system(1976) rule(880) can(841) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ data(3963) clinic(1234) research(1004) }
{ model(3480) simul(1196) paramet(876) }
{ bind(1733) structur(1185) ligand(1036) }
{ design(1359) user(1324) use(1319) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ compound(1573) activ(1297) structur(1058) }
{ cost(1906) reduc(1198) effect(832) }
{ first(2504) two(1366) second(1323) }
{ imag(2675) segment(2577) method(1081) }
{ extract(1171) text(1153) clinic(932) }
{ featur(1941) imag(1645) propos(1176) }
{ research(1218) medic(880) student(794) }
{ can(981) present(881) function(850) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ data(2317) use(1299) case(1017) }
{ data(3008) multipl(1320) sourc(1022) }
{ implement(1333) system(1263) develop(1122) }
{ decis(3086) make(1611) patient(1517) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ network(2748) neural(1063) input(814) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ concept(1167) ontolog(924) domain(897) }
{ control(1307) perform(991) simul(935) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ blood(1257) pressur(1144) flow(957) }
{ patient(2837) hospit(1953) medic(668) }
{ gene(2352) biolog(1181) express(1162) }
{ intervent(3218) particip(2042) group(1664) }
{ patient(1821) servic(1111) care(1106) }
{ health(1844) social(1437) communiti(874) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ result(1111) use(1088) new(759) }
{ process(1125) use(805) approach(778) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ data(1737) use(1416) pattern(1282) }
{ imag(1057) registr(996) error(939) }
{ sequenc(1873) structur(1644) protein(1328) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ assess(1506) score(1403) qualiti(1306) }
{ framework(1458) process(801) describ(734) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ method(1557) propos(1049) approach(1037) }
{ model(2220) cell(1177) simul(1124) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ use(976) code(926) identifi(902) }
{ drug(1928) target(777) effect(648) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

In systems biology, quantitative experimental data is the basis of building mathematical models. In most of the cases, they are stored in Excel files and hosted locally. To have a public database for collecting, retrieving and citing experimental raw data as well as experimental conditions is important for both experimentalists and modelers. However, the great effort needed in the data handling procedure and in the data submission procedure becomes the crucial limitation for experimentalists to contribute to a database, thereby impeding the database to deliver its benefit. Moreover, manual copy and paste operations which are commonly used in those procedures increase the chance of making mistakes. Excemplify, a web-based application, proposes a flexible and adaptable template-based solution to solve these problems. Comparing to the normal template based uploading approach, which is supported by some public databases, rather than predefining a format that is potentiall impractical, Excemplify allows users to create their own experiment-specific content templates in different experiment stages and to build corresponding knowledge bases for parsing. Utilizing the embedded knowledge of used templates, Excemplify is able to parse experimental data from the initial setup stage and generate following stages spreadsheets automatically. The proposed solution standardizes the flows of data traveling according to the standard procedures of applying the experiment, cuts down the amount of manual effort and reduces the chance of mistakes caused by manual data handling. In addition, it maintains the context of meta-data from the initial preparation manuscript and improves the data consistency. It interoperates and complements RightField and SEEK as well.

Resumo Limpo

system biolog quantit experiment data basi build mathemat model case store excel file host local public databas collect retriev cite experiment raw data well experiment condit import experimentalist model howev great effort need data handl procedur data submiss procedur becom crucial limit experimentalist contribut databas therebi imped databas deliv benefit moreov manual copi past oper common use procedur increas chanc make mistak excemplifi webbas applic propos flexibl adapt templatebas solut solv problem compar normal templat base upload approach support public databas rather predefin format potential impract excemplifi allow user creat experimentspecif content templat differ experi stage build correspond knowledg base pars util embed knowledg use templat excemplifi abl pars experiment data initi setup stage generat follow stage spreadsheet automat propos solut standard flow data travel accord standard procedur appli experi cut amount manual effort reduc chanc mistak caus manual data handl addit maintain context metadata initi prepar manuscript improv data consist interoper complement rightfield seek well

Resumos Similares

J Chem Inf Model - Design of novel FLT-3 inhibitors based on dual-layer 3D-QSAR model and fragment-based compounds in silico. ( 0,700480758436872 )
Int J Med Inform - Design and implementation of I2Vote--an interactive image-based voting system using windows mobile devices. ( 0,624221522900732 )
BMC Med Inform Decis Mak - Modeling healthcare authorization and claim submissions using the openEHR dual-model approach. ( 0,600496633938903 )
J Chem Inf Model - GRID-based three-dimensional pharmacophores II: PharmBench, a benchmark data set for evaluating pharmacophore elucidation methods. ( 0,599550435551267 )
Comput. Aided Surg. - Efficacy and accuracy of a novel rapid prototyping drill template for cervical pedicle screw placement. ( 0,591966065613238 )
Int J Comput Assist Radiol Surg - Hybrid image visualization tool for 3D integration of CT coronary anatomy and quantitative myocardial perfusion PET. ( 0,57269349510465 )
J Chem Inf Model - iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach. ( 0,5692539078039 )
Comput Biol Chem - Homology modeling, binding site identification and docking in flavone hydroxylase CYP105P2 in Streptomyces peucetius ATCC 27952. ( 0,563167077479816 )
Brief. Bioinformatics - RNA tertiary structure prediction with ModeRNA. ( 0,562031736449308 )
Neural Comput - Molecular diffusion model of neurotransmitter homeostasis around synapses supporting gradients. ( 0,554391865917242 )
J Med Syst - Knowledge extraction algorithm for variances handling of CP using integrated hybrid genetic double multi-group cooperative PSO and DPSO. ( 0,552308457959336 )
J Chem Inf Model - 3-D QSAutogrid/R: an alternative procedure to build 3-D QSAR models. Methodologies and applications. ( 0,550989849547249 )
Comput Methods Programs Biomed - Numerical framework to model temporally resolved multi-stage dynamic systems. ( 0,547647046019661 )
J Chem Inf Model - Three useful dimensions for domain applicability in QSAR models using random forest. ( 0,545189100409976 )
J. Comput. Biol. - Rich parameterization improves RNA structure prediction. ( 0,543842224732202 )
J Chem Inf Model - Template CoMFA applied to 116 biological targets. ( 0,543159406422141 )
Int J Comput Assist Radiol Surg - Multi-contrast unbiased MRI atlas of a Parkinson's disease population. ( 0,541344153984776 )
Int J Comput Assist Radiol Surg - MIDG-Emerging grid technologies for multi-site preclinical molecular imaging research communities. ( 0,536575646353963 )
J Chem Inf Model - Improving similarity-driven library design: customized matching and regioselective feature trees. ( 0,534780644904293 )
J Chem Inf Model - Conformer generation with OMEGA: learning from the data set and the analysis of failures. ( 0,534058375197985 )
J Chem Inf Model - In silico prediction of aqueous solubility using simple QSPR models: the importance of phenol and phenol-like moieties. ( 0,5316478993348 )
J. Med. Internet Res. - Staging dementia from symptom profiles on a care partner website. ( 0,530337918206699 )
J Chem Inf Model - Pharmacophore assessment through 3-D QSAR: evaluation of the predictive ability on new derivatives by the application on a series of antitubercular agents. ( 0,529834430738784 )
J Chem Inf Model - Impact of template choice on homology model efficiency in virtual screening. ( 0,527802199875019 )
J Chem Inf Model - A new approach to radial basis function approximation and its application to QSAR. ( 0,526679537820358 )
AMIA Annu Symp Proc - ASLForm: an adaptive self learning medical form generating system. ( 0,525308483555245 )
J Chem Inf Model - APL@Voro: a Voronoi-based membrane analysis tool for GROMACS trajectories. ( 0,522226987152959 )
J Chem Inf Model - Kinome-wide activity modeling from diverse public high-quality data sets. ( 0,522031083137522 )
J Chem Inf Model - Template CoMFA: the 3D-QSAR Grail? ( 0,520818276569788 )
J Biomed Inform - Mutual information-based template matching scheme for detection of breast masses: from mammography to digital breast tomosynthesis. ( 0,520630534494645 )
Brief. Bioinformatics - Software applications for flux balance analysis. ( 0,520552783637419 )
J Chem Inf Model - Comparative studies on some metrics for external validation of QSPR models. ( 0,520068063860157 )
J Chem Inf Model - Managing the computational chemistry big data problem: the ioChem-BD platform. ( 0,519171858768375 )
J Chem Inf Model - Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps (LiCABEDS) and its application on modeling ligand functionality for 5HT-subtype GPCR families. ( 0,519018821973111 )
J Chem Inf Model - Generalized workflow for generating highly predictive in silico off-target activity models. ( 0,517711081137202 )
J Chem Inf Model - CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. ( 0,516692498304815 )
Int J Comput Assist Radiol Surg - TREK: an integrated system architecture for intraoperative cone-beam CT-guided surgery. ( 0,513040283368131 )
J Am Med Inform Assoc - Validation of a common data model for active safety surveillance research. ( 0,512575717949604 )
J Chem Inf Model - ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 9. Extensible thermodynamic constraints for pure compounds and new model developments. ( 0,511985417608113 )
J Am Med Inform Assoc - Harvest: an open platform for developing web-based biomedical data discovery and reporting applications. ( 0,511399593517762 )
Int J Health Geogr - Defining socially-based spatial boundaries in the region of Peel, Ontario, Canada. ( 0,507867121746132 )
J Chem Inf Model - Best of both worlds: combining pharma data and state of the art modeling technology to improve in Silico pKa prediction. ( 0,505603502413305 )
Int J Med Inform - Application of a model based on fuzzy logic for evaluating nursing diagnostic accuracy of students. ( 0,504992283367763 )
J Chem Inf Model - Robust scoring functions for protein-ligand interactions with quantum chemical charge models. ( 0,503613812265924 )
Methods Inf Med - Platform for efficient switching between multiple devices in the intensive care unit. ( 0,502740512006598 )
J Chem Inf Model - Exploiting structural information in patent specifications for key compound prediction. ( 0,502503385570339 )
J Am Med Inform Assoc - Automated extraction of ejection fraction for quality measurement using regular expressions in Unstructured Information Management Architecture (UIMA) for heart failure. ( 0,502193184673487 )
Comput. Aided Surg. - Evaluation of a computational model to predict elbow range of motion. ( 0,501509383798526 )
Comput. Biol. Med. - A prediction model of substrates and non-substrates of breast cancer resistance protein (BCRP) developed by GA-CG-SVM method. ( 0,501290788547212 )
Comput. Biol. Med. - Numerical investigation of regional particle deposition in the upper airway of a standing male mannequin in calm air surroundings. ( 0,500505128277636 )
J Chem Inf Model - Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening. ( 0,500171401895184 )
IEEE Trans Neural Netw Learn Syst - Incremental Generalized Discriminative Common Vectors for Image Classification. ( 0,498737902909253 )
J Chem Inf Model - Three-dimensional pharmacophore modeling of liver-X receptor agonists. ( 0,497640242493072 )
Med Biol Eng Comput - Application of the RIMARC algorithm to a large data set of action potentials and clinical parameters for risk prediction of atrial fibrillation. ( 0,496805230118208 )
Methods Inf Med - Supporting translational research on inherited cardiomyopathies through information technology. ( 0,496719450349201 )
J Chem Inf Model - Integrated project views: decision support platform for drug discovery project teams. ( 0,495871654828758 )
Int J Med Inform - Evaluation of software maintain ability with open EHR - a comparison of architectures. ( 0,49467444852528 )
J Chem Inf Model - Combined 3D-QSAR, molecular docking, and molecular dynamics study on piperazinyl-glutamate-pyridines/pyrimidines as potent P2Y12 antagonists for inhibition of platelet aggregation. ( 0,494300773352962 )
J Chem Inf Model - Combined receptor and ligand-based approach to the universal pharmacophore model development for studies of drug blockade to the hERG1 pore domain. ( 0,493532576882185 )
J Chem Inf Model - Study of chromatographic retention of natural terpenoids by chemoinformatic tools. ( 0,492659616705864 )
AMIA Annu Symp Proc - Target Contour Testing/Instructional Computer Software (TaCTICS): A Novel Training and Evaluation Platform for Radiotherapy Target Delineation. ( 0,491915030080507 )
J Chem Inf Model - Profile-QSAR: a novel meta-QSAR method that combines activities across the kinase family to accurately predict affinity, selectivity, and cellular activity. ( 0,491283375251993 )
Artif Intell Med - Fuzzy model identification of dengue epidemic in Colombia based on multiresolution analysis. ( 0,490779315190503 )
J Chem Inf Model - Building a three-dimensional model of CYP2C9 inhibition using the Autocorrelator: an autonomous model generator. ( 0,489397874443974 )
Med Biol Eng Comput - Development of a comprehensive musculoskeletal model of the shoulder and elbow. ( 0,489234619895201 )
Brief. Bioinformatics - Protein mass spectra data analysis for clinical biomarker discovery: a global review. ( 0,487827382557609 )
J Chem Inf Model - Jointly handling potency and toxicity of antimicrobial peptidomimetics by simple rules from desirability theory and chemoinformatics. ( 0,487728653590961 )
Med Biol Eng Comput - Accelerometry-based prediction of movement dynamics for balance monitoring. ( 0,486658850568688 )
Comput Methods Programs Biomed - Predicting body fat percentage based on gender, age and BMI by using artificial neural networks. ( 0,486443472823156 )
J Am Med Inform Assoc - BiobankConnect: software to rapidly connect data elements for pooled analysis across biobanks using ontological and lexical indexing. ( 0,485893800844469 )
J Chem Inf Model - Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets. ( 0,484089468270052 )
J Chem Inf Model - Development of novel 3D-QSAR combination approach for screening and optimizing B-Raf inhibitors in silico. ( 0,484053074670161 )
J Chem Inf Model - Automated building of organometallic complexes from 3D fragments. ( 0,484010491538871 )
J Chem Inf Model - MOSAIC: a data model and file formats for molecular simulations. ( 0,483520099296053 )
Comput. Biol. Med. - Artificial neural network modelling of the results of tympanoplasty in chronic suppurative otitis media patients. ( 0,482986001155494 )
J Chem Inf Model - Computational derivation of structural alerts from large toxicology data sets. ( 0,482756401716819 )
J Chem Inf Model - Kinase-kernel models: accurate in silico screening of 4 million compounds across the entire human kinome. ( 0,482158062911435 )
Med Biol Eng Comput - Share and enjoy: anatomical models database--generating and sharing cardiovascular model data using web services. ( 0,48189502077355 )
J Chem Inf Model - AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles. ( 0,481703794249858 )
J Biomed Inform - Model-driven approach to data collection and reporting for quality improvement. ( 0,479619650454781 )
J Chem Inf Model - Introducing conformal prediction in predictive modeling. A transparent and flexible alternative to applicability domain determination. ( 0,47949047870929 )
Curr Comput Aided Drug Des - QSAR Models for the Reactivation of Sarin Inhibited AChE by Quaternary Pyridinium Oximes Based on Monte Carlo Method. ( 0,479351637399928 )
Artif Intell Med - Training artificial neural networks directly on the concordance index for censored data using genetic algorithms. ( 0,479215984773017 )
Health Informatics J - Implementation of integrated heterogeneous electronic electrocardiography data into Maharaj Nakorn Chiang Mai Hospital Information System. ( 0,47864090069456 )
Int J Comput Assist Radiol Surg - Guided implant surgery on oral cancer patients: in vitro study. ( 0,478421805532916 )
J Chem Inf Model - Coping with unbalanced class data sets in oral absorption models. ( 0,477772874827973 )
Comput. Biol. Med. - IVUSAngio tool: a publicly available software for fast and accurate 3D reconstruction of coronary arteries. ( 0,477047898013562 )
J Chem Inf Model - Ligand-optimized homology models of D1 and D2 dopamine receptors: application for virtual screening. ( 0,476984159089137 )
J Chem Inf Model - Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection. ( 0,47687639415873 )
IEEE Trans Neural Netw Learn Syst - A Unified Framework for Data Visualization and Coclustering. ( 0,476473532346789 )
J Chem Inf Model - Doing a good turn: the use of quaternions for rotation in molecular docking. ( 0,475692299599061 )
Brief. Bioinformatics - Joint analysis of miRNA and mRNA expression data. ( 0,475661069936834 )
J Med Syst - Accuracy enhancement in a fuzzy expert decision making system through appropriate determination of membership functions and its application in a medical diagnostic decision making system. ( 0,475498438148268 )
Comput Methods Programs Biomed - Interstitial insulin kinetic parameters for a 2-compartment insulin model with saturable clearance. ( 0,475128192629116 )
J Chem Inf Model - Ligand-based target prediction with signature fingerprints. ( 0,473186508197408 )
Int J Med Robot - Noninvasive ultrasonic measuring system for bone geometry examination. ( 0,473154080479904 )
J Chem Inf Model - Improvement of virtual screening results by docking data feature analysis. ( 0,472404512220219 )
J Chem Inf Model - Beyond the scope of Free-Wilson analysis: building interpretable QSAR models with machine learning algorithms. ( 0,471877374422409 )
Appl Clin Inform - Design and multicentric implementation of a generic software architecture for patient recruitment systems re-using existing HIS tools and routine patient data. ( 0,47167141143268 )
Med Biol Eng Comput - Optimal design of clinical tests for the identification of physiological models of type 1 diabetes in the presence of model mismatch. ( 0,471646237073108 )