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 Informatics term index

Evolving Terminology for Emerging Technologies
Comments? Questions? Revisions? Mary Chitty mchitty@healthtech.com
Last revised October 04, 2019

Roger Brent said in his opening remarks for the 2000 After the Genome meeting in Jackson Hole Wyoming "current efforts to come to grips with genomic information often resemble computer-savvy library science, where the most important issues concern categories, classification schemes and information retrieval … What we would actually like to achieve, however, is a predictive understanding of biological function. The goal here is a true computational biology that will be able to make functional predictions from available genomic data [italics added] http://www.atgx.org/info_gruber.html     

Not a comprehensive list of terms, but a quick and dirty finding aid while I'm working on getting these glossaries into a (long overdue) searchable database. 
Biology terms index  Chemistry term index   Drug discovery & development terms index  Healthcare term index   Technologies terms index  

Algorithms algorithm, ANOVA, bootstrapping, chaos theory, cluster... , coefficient of variation, curse of dimensionality, data ming, data warehouse, decision tree, dendrogram, dimensionality, evolutionary computation, expert systems, fuzzy, Generative Adversarial Networks GANS, genetic algorithms, genetic programming, Hansch analysis, heat map, heuristic, ill- posed problems, information theory, Knowledge Discovery in Databases KDD, latent variables, MathML, Monte Carlo, normalization, OASIS, parsing, pattern recognition, Principal Components Analysis PCA, probability, recursive partitioning, regression to the mean, schema, schemata, self-organization, self- organizing, SIMCA, thresholding, training set, well posed problem  Focus is on statistical and computational approaches to data organization, structured data

Bioinformatics annotation, BISTI, BSML, bio...., computational ..., curated, databases, EBI, federated, functional bioinformatics, molecular bioinformatics, NCBI, non-redundant, pharmaceutical bioinformatics, spatio temporal dynamics, standards, structured data, wrappers. Focus is on databases, analyzing sequences and trying to integrate heterogeneous biological data, unstructured data. Primarily a subset of Drug discovery informatics.

Cheminformatics/Chemoinformatics CoMFA Comparative Molecular Field Analysis,  chemical informatics, chemical information..., chemometrics, drug design,  information silos, "plug and play", rules of five, silo systems, SAR, structure based drug design, virtual...  Subset of Drug discovery informatics. See also Chemistry, Pharmaceutical Biology 

Clinical & Medical Informatics : adaptive clinical trials, AI for healthcare, Bayesian clinical trials, Bayesian networks, biomathematics, biomedical informatics, case definitions, CDISC, clinical data repositories, clinical forecasting,  clinical informatics, clinical research, clinomics, cohort studies, communications standards, comparative effectiveness research, complex diseases, computational phenotypes, computational physiology, computational therapeutics, consumer health informatics, digital health, digital therapeutics, drug utilization, e-health, electronic data capture, electronic medical records, electronic prescribing, electronic records FDA, evidence based medicine, genomic epidemiology, health informatics, health IT tools, health record, healthcare informatics, HL7 Health Level 7, human factors, immunoinformatics, in silico clinical trial, in silico pharmacology, laboratory informatics, LOINC Logical Observation Identifiers Names and Codes, meaningful use, medical bioinformatics, medical informatics, MEDRA, meta-analysis, meta-regression mHealth mobile health, National Center for Integrative Biomedical Informatics, National Electronic clinical Trials and Research NECTAR, neuroimaging, neuroinformatics, Office of the National Coordinator for Health Information Technology (ONC), outcomes research, pathology informatics, patient engagement, patient reported outcomes, Personal Health Record PHR, pharmacoepidemiology, population health, predictive genomics, predictive pharmacogenomics, prognosis, public health informatics, Real World Data RWD, Real World Evidence RWE, systems medicine, sydromics, telehealth, telemedicine,  SNOMED, UMLS, uncertainty, universal trial number

Databases & software directory Brief descriptions of 300+ databases, 30+ software programs 

Data Science & Machine Learning  AI Trends, artificial intelligence, artificial general intelligence AGI, artificial narrow intelligence ANI, artificial super intelligence ASI, augmented intelligence, big data, clinical trials and big data, cognitive computing, data curation, data dredging, data driven decision making,  data lake, data quality, data science, data scientist, data stewardship, data storytelling, data swamp, data translation, data visualization, deep learning, deep machine learning, FAIR data findable accessible, interoperable, reusable; GO FAIR, Hadoop, heavy quants light quants, heuristic, just in time information retrieval, machine intelligence, machine learning, neural networks, Neural Networks Artificial, open science, overfitting, pattern recognition, predictive analytics, Python, R, reinforcement learning, robust, software as a medical device, stochastic, supervised machine learning, Support Vector Machine SVMs, training sets, unsupervised learning

Drug discovery informatics   Biosemantics Group, CADD Computer Assisted Drug Design, computational drug design..., de novo design, drug design, eScience Lab, in silico ..., LIMS Laboratory Information Management Systems, molecular informatics, molecular mimicry, NeuroCommons, pharmacometrics, rational drug design, receptor mapping, simulations, soft drug design, structure-based drug design, synthetic biology, virtual screening See also Cheminformatics

Genomic informatics  ab initio gene, AI for genomics, alignment, assembled, biocomputing, biological computing, BLAST, comparative genome annotation, complex genomes, computational gene recognition, computational genomics, concordance, consensus sequence, conserved sequence, contig... DDBJ, deep homology, discordance, distributed sequence annotation, DNA computers, DNA computing, Ensembl, exon parsing, exon prediction, exon shuffling, extreme phenotype selection studies, false negative, false positive, filtering, finished sequence, fold change, gap, GenBank, gene finding, gene identification, gene parsing, gene prediction, gene recognition, genetic association studies, genome annotation, genome assembly, genome informatics, genome misassembly, genomic computing, genomic data, GRAIL, global normalization, GWAS Genome Wide Association Studies, high throughput nucleotide sequencing analysis, homologue, homologous, homology, International Nucleotide Database, local alignment, log ratios, MAGE, MAML, MGED, MIAME, microarray analysis techniques, microarrays data analysis, microarrays image analysis, microarray informatics, mismatches, molecular sequence annotation, noise characterization, normality, normalization, oligonucleotide array sequence analysis, ORF prediction, Phred .. , reverse transfection, RNA sequence analysis, scaffolds, sequence alignment, sequence homology, sequence ontology, sequencing algorithm, similarity search, Smith Waterman alignment

Informatics overview: 3D QSAR; bioinformatics, BioIT, bleeding edge, bottom-up, cheminformatics, chemoinformatics, clinical informatics, complexity, computational biophysics, data mining, data scientist, databases, deep learning, determinism, digital health, electronic health records, Gene Ontology GO, genome informatics, Good Information Practices Document, health informatics, in silico, informatics,  information overload, information technology, interdisciplinary, interoperability, "just in time" information, life sciences informatics, Linked Data, machine learning, medical informatics, metadata, molecular modeling, new paradigms, nonlinear, normalization, ontology, predictive analytics, public health informatics, semantic web, semantics, social informatics, taxonomies, text mining, top-down, XML 

Information management & interpretation 3D technologies, bias, collaborative filtering, collaborative metadata, computational linguistics, data management, data mapping, data mining, data munging, data quality, data transfer, data visualization, deep web, description logic, digitization, disambiguation, Dublin Core, evolvability, federated databases, federated information system, fractal nature of web, granularity, informatics, information architecture, ecology, extraction, harvesting, integration, overload, retrieval, visualization; invisible web, knowledge integration,  knowledge management, lexical semantics, lexicon, linked data, markup languages, mash up, NISO, precision, query contraction, query expansion, recall, relevance, remembrance agents, SOAP Simple Object Access Protocol, social informatics, soft computing, term extraction, term mining, text mining, unstructured data, variance, visualization, W3C, web, web services interoperability, web services web like, workflows.  Focus is on combinations of human and automated data and information management, retrieval and interpretation.  See also Data science and machine learning

IT infrastructure  AWS Amazon Web Services, blockchain,  CORBA, computation, computers, computing – amorphous, Beowulf, cloud, data; configurable, customizable, data storage, edge computing, FLOPs, geek, Google Custom search APIs & tools, grid computing, Hadoop, HPC High Performance Computing, legacy systems,  Linux, markup languages, metacomputer, modularity, molecular computer, middleware, Moore's Law, open source, peta, petaflop, quantum computing, quantum informatics, supercomputers, teraFlop, utility computing   Focus is on hardware.

Ontologies & Taxonomies  application ontologies, biomedical databases, biomedical ontologies, biomedical ontology recommender, bio-ontologies, BioPax, BioPortal, bottom up…, canonical ontologies, classification, clinical ontologies, common ontology, controlled vocabularies, core ontology, data munging, data wrangling, descriptive logic ontology, descriptive & prescriptive ontologies, descriptive taxonomy, Directed Acyclic Graph DAG, domain ontology, dynamic ontology, dynamic taxonomy, facet, faceted…, FAIR data, folksonomy, formal ontology, game ontology, global ontology,  GO Gene Ontology, heavyweight ontology, hierarchy, interoperability, knowledge graph, lightweight ontology, linked data, metadata, middle ontologies, mixed ontologies, National Center for Biomedical Ontologies NCBO, navigational ontologies, navigational taxonomies, natural language processing, ontological commitment, ontologies proteomics, ,ontology  ontologies, ontology mapping, Open Biological & Biomedical Foundry OBO, open standard, orthogonal taxonomies OWL Web Ontology Language, OXO, reference ontologies, relationships, reproducibility crisis, Resource Description Framework RDF, reusable ontology, semantic heterogeneity, semantic interoperability, semantic web, semantics, shared ontologies, share taxonomies,  SKOS Simple Knowledge Organization System, soft ontology, structural heterogeneity, syntactic relationships, syntax, tag cloud, tagging, taxonomies, terminological ontology, Terminology Forum, thesaurus, top down bottom up ontologies, top down taxonomy, topic maps, triple, upper ontology, vaccine ontology, vocabularies, W3C data activity, weak ontology, XML Extensible Markup Language

Protein informatics  ab initio protein, ab initio quantum ..., annotation proteins, CASP Critical Assessment of protein Structure Prediction , computational biophysics, docking... , domain shuffling, energy function, fold alignment, fold recognition, Hidden Markov Models, homeomorphic superfamilies, homology domains, homology models,  interologs, molecular recognition, Monte Carlo techniques, post translational modification identification, protein analysis sequencing, protein array analysis, protein bioinformatics, protein computational tools, protein databases, protein dynamics, protein function, protein identification, protein informatics, protein interactions, protein mRNA data, protein networks, protein sequence, protein sequence space, protein sorting signals, protein structure prediction, proteogenomics, regulatory homology, RNA structural genomics, Rosetta stone method, sequence homology amino acid, sequence similarity searching, similarity, structural bioinformatics, structural genomics, structural homology, structural proteomics, structure based design, structure based drug design, structure prediction, threading, virtual genomes, whole proteome data mining. See also Drug discovery informatics

Research applied research, basic research, biomedical research, bleeding edge, bottom up,  cutting edge, data sharing, Delphi technique, development, Early stage investigator policies, experimental design, HIPAA, high risk high reward research, holism, Horizon 2020, hypothesis driven, information silos, interdisciplinary, kilogram, longitudinal research, Next generation researchers Initiative, meta-analysis, nominal group technique, paradigm, peer review, R&D,  reductionism, research joint ventures, top down, truth  

Informatics resources
Informatics Conferences http://www.healthtech.com/conferences/upcoming.aspx?s=NFO
BioIT World Expo http://www.bio-itworldexpo.com/
Molecular Medicine Tri Conference http://www.triconference.com/
Informatics Short courses http://www.healthtech.com/Conferences_Upcoming_ShortCourses.aspx?s=NFO

BioIT World magazine http://www.bio-itworld.com/   
BioIT World archives http://www.bio-itworld.com/BioIT/BioITArchive.aspx
BioIT World podcasts http://www.bio-itworld.com/podcasts/
BioIT World White papers & special reports  http://www.bio-itworld.com/BioIT/WhitePapers.aspx
Clinical Research News http://www.clinicalinformaticsnews.com/

How to look for other unfamiliar  terms