Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination.

BACKGROUND: LINCS, "Library of Integrated Network-based Cellular Signatures", and IDG, "Illuminating the Druggable Genome", are both NIH projects and consortia that have generated rich datasets for the study of the molecular basis of human health and disease. LINCS L1000 expression signatures provide unbiased systems/omics experimental evidence. IDG provides compiled and curated knowledge for illumination and prioritization of novel drug target hypotheses. Together, these resources can support a powerful new approach to identifying novel drug targets for complex diseases, such as Parkinson's disease (PD), which continues to inflict severe harm on human health, and resist traditional research approaches. RESULTS: Integrating LINCS and IDG, we built the Knowledge Graph Analytics Platform (KGAP) to support an important use case: identification and prioritization of drug target hypotheses for associated diseases. The KGAP approach includes strong semantics interpretable by domain scientists and a robust, high performance implementation of a graph database and related analytical methods. Illustrating the value of our approach, we investigated results from queries relevant to PD. Approved PD drug indications from IDG's resource DrugCentral were used as starting points for evidence paths exploring chemogenomic space via LINCS expression signatures for associated genes, evaluated as target hypotheses by integration with IDG. The KG-analytic scoring function was validated against a gold standard dataset of genes associated with PD as elucidated, published mechanism-of-action drug targets, also from DrugCentral. IDG's resource TIN-X was used to rank and filter KGAP results for novel PD targets, and one, SYNGR3 (Synaptogyrin-3), was manually investigated further as a case study and plausible new drug target for PD. CONCLUSIONS: The synergy of LINCS and IDG, via KG methods, empowers graph analytics methods for the investigation of the molecular basis of complex diseases, and specifically for identification and prioritization of novel drug targets. The KGAP approach enables downstream applications via integration with resources similarly aligned with modern KG methodology. The generality of the approach indicates that KGAP is applicable to many disease areas, in addition to PD, the focus of this paper.

TIGA: target illumination GWAS analytics.

MOTIVATION: Genome-wide association studies can reveal important genotype-phenotype associations; however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study. RESULTS: Here, we describe rational ranking, filtering and interpretation of inferred gene-trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene-trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene-trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite relative citation ratio, and meanRank scores, to aggregate multivariate evidence.This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists. AVAILABILITY AND IMPLEMENTATION: Web application, datasets and source code via https://unmtid-shinyapps.net/tiga/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Netpredictor: R and Shiny package to perform drug-target network analysis and prediction of missing links.

BACKGROUND: Netpredictor is an R package for prediction of missing links in any given unipartite or bipartite network. The package provides utilities to compute missing links in a bipartite and well as unipartite networks using Random Walk with Restart and Network inference algorithm and a combination of both. The package also allows computation of Bipartite network properties, visualization of communities for two different sets of nodes, and calculation of significant interactions between two sets of nodes using permutation based testing. The application can also be used to search for top-K shortest paths between interactome and use enrichment analysis for disease, pathway and ontology. The R standalone package (including detailed introductory vignettes) and associated R Shiny web application is available under the GPL-2 Open Source license and is freely available to download. RESULTS: We compared different algorithms performance in different small datasets and found random walk supersedes rest of the algorithms. The package is developed to perform network based prediction of unipartite and bipartite networks and use the results to understand the functionality of proteins in an interactome using enrichment analysis. CONCLUSION: The rapid application development envrionment like shiny, helps non programmers to develop fast rich visualization apps and we beleieve it would continue to grow in future with further enhancements. We plan to update our algorithms in the package in near future and help scientist to analyse data in a much streamlined fashion.

Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus.

Tuberculosis (TB) is still a major global health challenge, killing over 1.5 million people each year, and hence, there is a need to identify and develop novel treatments for Mycobacterium tuberculosis (M. tuberculosis). The prevalence of infections caused by nontuberculous mycobacteria (NTM) is also increasing and has overtaken TB cases in the United States and much of the developed world. Mycobacterium abscessus (M. abscessus) is one of the most frequently encountered NTM and is difficult to treat. We describe the use of drug-disease association using a semantic knowledge graph approach combined with machine learning models that has enabled the identification of several molecules for testing anti-mycobacterial activity. We established that niclosamide (M. tuberculosis IC90 2.95 µM; M. abscessus IC90 59.1 µM) and tribromsalan (M. tuberculosis IC90 76.92 µM; M. abscessus IC90 147.4 µM) inhibit M. tuberculosis and M. abscessus in vitro. To investigate the mode of action, we determined the transcriptional response of M. tuberculosis and M. abscessus to both compounds in axenic log phase, demonstrating a broad effect on gene expression that differed from known M. tuberculosis inhibitors. Both compounds elicited transcriptional responses indicative of respiratory pathway stress and the dysregulation of fatty acid metabolism.

Assessing drug target association using semantic linked data.

The rapidly increasing amount of public data in chemistry and biology provides new opportunities for large-scale data mining for drug discovery. Systematic integration of these heterogeneous sets and provision of algorithms to data mine the integrated sets would permit investigation of complex mechanisms of action of drugs. In this work we integrated and annotated data from public datasets relating to drugs, chemical compounds, protein targets, diseases, side effects and pathways, building a semantic linked network consisting of over 290,000 nodes and 720,000 edges. We developed a statistical model to assess the association of drug target pairs based on their relation with other linked objects. Validation experiments demonstrate the model can correctly identify known direct drug target pairs with high precision. Indirect drug target pairs (for example drugs which change gene expression level) are also identified but not as strongly as direct pairs. We further calculated the association scores for 157 drugs from 10 disease areas against 1683 human targets, and measured their similarity using a [Formula: see text] score matrix. The similarity network indicates that drugs from the same disease area tend to cluster together in ways that are not captured by structural similarity, with several potential new drug pairings being identified. This work thus provides a novel, validated alternative to existing drug target prediction algorithms. The web service is freely available at: http://chem2bio2rdf.org/slap.

Optimizing Virtual Health Technologies Through a Performance-based Readiness Model: Lessons From the Field Deployment of National Emergency Tele-Critical Care Network.

INTRODUCTION: The advancement of the Army's National Emergency Tele-Critical Care Network (NETCCN) and planned evolution to an Intelligent Medical System rest on a digital transformation characterized by the application of analytic rigor anchored and machine learning.The goal is an enduring capability for telecritical care in support of the Nation's warfighters and, more broadly, for emergency response, crisis management, and mass casualty situations as the number and intensity of disasters increase nationwide. That said, technology alone is unlikely to solve the most pressing issues in operational medicine and combat casualty care. MATERIALS AND METHODS: A total performance system (TPS) creates opportunities to address vulnerabilities and overcome barriers to success. As applied during the NETCCN project, the TPS captures the best performance-centric information and know-how, increasing the potential to save lives, improve readiness, and accomplish missions. RESULTS: The purpose of this project was to apply a performance-based readiness model to aid in the evaluation of Army telehealth technologies. Through various user-facing surveys, polls, and reporting techniques, the project aimed to measure the perceived value of telehealth technologies within a sample of the project team member population. By providing a detailed approach to the collection of lessons learned, researchers were able to determine the importance of information and methods versus a focus on technology alone. The use of an emoji-based feedback assessment indicated that most lessons learned were helpful to the project team. CONCLUSIONS: Through the NETCCN TPS, we have been able to address product-related measures, knowledge of product efficacy, project metrics, and many implementation considerations that can be further investigated by setting and engagement type. Through the Technology in Disaster Environments learning accelerator, it was possible to rapidly acquire, process, organize, and disseminate best practices and learnings in near real time, providing a critical feedback and improvement loop.

Project APRED: A web-based data analytics platform for supporting community disaster resilience.

In this paper, we introduce the Analysis Platform for Risk, Resilience, and Expenditure in Disasters (APRED)-a disaster-analytic platform developed for crisis practitioners and economic developers across the United States (US). APRED provides practitioners with a centralized platform for exploring disaster resilience and vulnerability profiles of all counties across the US. The platform comprises five sections including: (1) Disaster Resilience Index, (2) Business Vulnerability Index, (3) Disaster Declaration History, (4) County Profile, and (5) Storm History sections. We further describe our end-to-end human-centered design and engineering process that involved contextual inquiry, community-based participatory design, and rapid prototyping with the support of US Economic Development Administration representatives and regional economic developers across the US. Findings from our study revealed that distributed cognition, content heuristic, shareability, and human-centered systems are crucial considerations for developing data-intensive visualization platforms for resilience planning. We discuss the implications of these findings and inform future research on developing sociotechnical visualization platforms to support resilience planning.

Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology.

MOTIVATION: Networks to predict protein pharmacology can be created using ligand similarity or using known bioassay response profiles of ligands. Recent publications indicate that similarity methods can be highly accurate, but it has been unclear how similarity methods compare to methods that use bioassay response data directly. RESULTS: We created protein networks based on ligand similarity (Similarity Ensemble Approach or SEA) and ligand bioassay response-data (BARD) using 155 Pfizer internal BioPrint assays. Both SEA and BARD successfully cluster together proteins with known relationships, and predict some non-obvious relationships. Although the approaches assess target relations from different perspectives, their networks overlap considerably (40% overlap of the top 2% of correlated edges). They can thus be considered as comparable methods, with a distinct advantage of the similarity methods that they only require simple computations (similarity of compound) as opposed to extensive experimental data. CONTACTS: djwild@indiana.edu; eric.gifford@pfizer.com. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Semantic inference using chemogenomics data for drug discovery.

BACKGROUND: Semantic Web Technology (SWT) makes it possible to integrate and search the large volume of life science datasets in the public domain, as demonstrated by well-known linked data projects such as LODD, Bio2RDF, and Chem2Bio2RDF. Integration of these sets creates large networks of information. We have previously described a tool called WENDI for aggregating information pertaining to new chemical compounds, effectively creating evidence paths relating the compounds to genes, diseases and so on. In this paper we examine the utility of automatically inferring new compound-disease associations (and thus new links in the network) based on semantically marked-up versions of these evidence paths, rule-sets and inference engines. RESULTS: Through the implementation of a semantic inference algorithm, rule set, Semantic Web methods (RDF, OWL and SPARQL) and new interfaces, we have created a new tool called Chemogenomic Explorer that uses networks of ontologically annotated RDF statements along with deductive reasoning tools to infer new associations between the query structure and genes and diseases from WENDI results. The tool then permits interactive clustering and filtering of these evidence paths. CONCLUSIONS: We present a new aggregate approach to inferring links between chemical compounds and diseases using semantic inference. This approach allows multiple evidence paths between compounds and diseases to be identified using a rule-set and semantically annotated data, and for these evidence paths to be clustered to show overall evidence linking the compound to a disease. We believe this is a powerful approach, because it allows compound-disease relationships to be ranked by the amount of evidence supporting them.

Improving usability and accessibility of cheminformatics tools for chemists through cyberinfrastructure and education.

Some of the latest trends in cheminformatics, computation, and the world wide web are reviewed with predictions of how these are likely to impact the field of cheminformatics in the next five years. The vision and some of the work of the Chemical Informatics and Cyberinfrastructure Collaboratory at Indiana University are described, which we base around the core concepts of e-Science and cyberinfrastructure that have proven successful in other fields. Our chemical informatics cyberinfrastructure is realized by building a flexible, generic infrastructure for cheminformatics tools and databases, exporting "best of breed" methods as easily-accessible web APIs for cheminformaticians, scientists, and researchers in other disciplines, and hosting a unique chemical informatics education program aimed at scientists and cheminformatics practitioners in academia and industry.

Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data.

BACKGROUND: Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as Bio2RDF and LODD have tackled the problem of linking biological data and drug data respectively using RDF. Thus far, the inclusion of chemogenomic and systems chemical biology information that crosses the domains of chemistry and biology has been very limited RESULTS: We have created a single repository called Chem2Bio2RDF by aggregating data from multiple chemogenomics repositories that is cross-linked into Bio2RDF and LODD. We have also created a linked-path generation tool to facilitate SPARQL query generation, and have created extended SPARQL functions to address specific chemical/biological search needs. We demonstrate the utility of Chem2Bio2RDF in investigating polypharmacology, identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug reactions. CONCLUSIONS: We have created a new semantic systems chemical biology resource, and have demonstrated its potential usefulness in specific examples of polypharmacology, multiple pathway inhibition and adverse drug reaction--pathway mapping. We have also demonstrated the usefulness of extending SPARQL with cheminformatics and bioinformatics functionality.

RepTB: a gene ontology based drug repurposing approach for tuberculosis.

Tuberculosis (TB) is the world's leading infectious killer with 1.8 million deaths in 2015 as reported by WHO. It is therefore imperative that alternate routes of identification of novel anti-TB compounds are explored given the time and costs involved in new drug discovery process. Towards this, we have developed RepTB. This is a unique drug repurposing approach for TB that uses molecular function correlations among known drug-target pairs to predict novel drug-target interactions. In this study, we have created a Gene Ontology based network containing 26,404 edges, 6630 drug and 4083 target nodes. The network, enriched with molecular function ontology, was analyzed using Network Based Inference (NBI). The association scores computed from NBI are used to identify novel drug-target interactions. These interactions are further evaluated based on a combined evidence approach for identification of potential drug repurposing candidates. In this approach, targets which have no known variation in clinical isolates, no human homologs, and are essential for Mtb's survival and or virulence are prioritized. We analyzed predicted DTIs to identify target pairs whose predicted drugs may have synergistic bactericidal effect. From the list of predicted DTIs from RepTB, four TB targets, namely, FolP1 (Dihydropteroate synthase), Tmk (Thymidylate kinase), Dut (Deoxyuridine 5'-triphosphate nucleotidohydrolase) and MenB (1,4-dihydroxy-2-naphthoyl-CoA synthase) may be selected for further validation. In addition, we observed that in some cases there is significant chemical structure similarity between predicted and reported drugs of prioritized targets, lending credence to our approach. We also report new chemical space for prioritized targets that may be tested further. We believe that with increasing drug-target interaction dataset RepTB will be able to offer better predictive value and is amenable for identification of drug-repurposing candidates for other disease indications too.

Userscripts for the life sciences.

BACKGROUND: The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. RESULTS: Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. CONCLUSION: This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.

PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets.

BACKGROUND: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources. RESULTS: PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results. CONCLUSIONS: The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel "similar data items detection" algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust.

Challenges for chemoinformatics education in drug discovery.

Chemoinformatics is rapidly becoming a core part of drug design informatics, yet the educational opportunities in the field are currently limited. This article reviews the academic and commercial educational programs that are available in chemoinformatics, considers the current challenges and takes a look at emerging trends, such as distance education and intensive short courses.

An activity canyon characterization of the pharmacological topography.

BACKGROUND: Highly chemically similar drugs usually possess similar biological activities, but sometimes, small changes in chemistry can result in a large difference in biological effects. Chemically similar drug pairs that show extreme deviations in activity represent distinctive drug interactions having important implications. These associations between chemical and biological similarity are studied as discontinuities in activity landscapes. Particularly, activity cliffs are quantified by the drop in similar activity of chemically similar drugs. In this paper, we construct a landscape using a large drug-target network and consider the rises in similarity and variation in activity along the chemical space. Detailed analysis of structure and activity gives a rigorous quantification of distinctive pairs and the probability of their occurrence. RESULTS: We analyze pairwise similarity (s) and variation (d) in activity of drugs on proteins. Interactions between drugs are quantified by considering pairwise s and d weights jointly with corresponding chemical similarity (c) weights. Similarity and variation in activity are measured as the number of common and uncommon targets of two drugs respectively. Distinctive interactions occur between drugs having high c and above (below) average d (s). Computation of predicted probability of distinctiveness employs joint probability of c, s and of c, d assuming independence of structure and activity. Predictions conform with the observations at different levels of distinctiveness. Results are validated on the data used and another drug ensemble. In the landscape, while s and d decrease as c increases, d maintains value more than s. c ∈ [0.3, 0.64] is the transitional region where rises in d are significantly greater than drops in s. It is fascinating that distinctive interactions filtered with high d and low s are different in nature. It is crucial that high c interactions are more probable of having above average d than s. Identification of distinctive interactions is better with high d than low s. These interactions belong to diverse classes. d is greatest between drugs and analogs prepared for treatment of same class of ailments but with different therapeutic specifications. In contrast, analogs having low s would treat ailments from distinct classes. CONCLUSIONS: Intermittent spikes in d along the axis of c represent canyons in the activity landscape. This new representation accounts for distinctiveness through relative rises in s and d. It provides a mathematical basis for predicting the probability of occurrence of distinctiveness. It identifies the drug pairs at varying levels of distinctiveness and non-distinctiveness. The predicted probability formula is validated even if data approximately satisfy the conditions of its construction. Also, the postulated independence of structure and activity is of little significance to the overall assessment. The difference in distinctive interactions obtained by s and d highlights the importance of studying both of them, and reveals how the choice of measurement can affect the interpretation. The methods in this paper can be used to interpret whether or not drug interactions are distinctive and the probability of their occurrence. Practitioners and researchers can rely on this identification for quantitative modeling and assessment.

Optimizing drug-target interaction prediction based on random walk on heterogeneous networks.

BACKGROUND: Predicting novel drug-target associations is important not only for developing new drugs, but also for furthering biological knowledge by understanding how drugs work and their modes of action. As more data about drugs, targets, and their interactions becomes available, computational approaches have become an indispensible part of drug target association discovery. In this paper we apply random walk with restart (RWR) method to a heterogeneous network of drugs and targets compiled from DrugBank database and investigate the performance of the method under parameter variation and choice of chemical fingerprint methods. RESULTS: We show that choice of chemical fingerprint does not affect the performance of the method when the parameters are tuned to optimal values. We use a subset of the ChEMBL15 dataset that contains 2,763 associations between 544 drugs and 467 target proteins to evaluate our method, and we extracted datasets of bioactivity ≤1 and ≤10 µM activity cutoff. For 1 µM bioactivity cutoff, we find that our method can correctly predict nearly 47, 55, 60% of the given drug-target interactions in the test dataset having more than 0, 1, 2 drug target relations for ChEMBL 1 µM dataset in top 50 rank positions. For 10 µM bioactivity cutoff, we find that our method can correctly predict nearly 32.4, 34.8, 35.3% of the given drug-target interactions in the test dataset having more than 0, 1, 2 drug target relations for ChEMBL 1 µM dataset in top 50 rank positions. We further examine the associations between 110 popular top selling drugs in 2012 and 3,519 targets and find the top ten targets for each drug. CONCLUSIONS: We demonstrate the effectiveness and promise of the approach-RWR on heterogeneous networks using chemical features-for identifying novel drug target interactions and investigate the performance.

Novel Phenotypic Outcomes Identified for a Public Collection of Approved Drugs from a Publicly Accessible Panel of Assays.

Phenotypic assays have a proven track record for generating leads that become first-in-class therapies. Whole cell assays that inform on a phenotype or mechanism also possess great potential in drug repositioning studies by illuminating new activities for the existing pharmacopeia. The National Center for Advancing Translational Sciences (NCATS) pharmaceutical collection (NPC) is the largest reported collection of approved small molecule therapeutics that is available for screening in a high-throughput setting. Via a wide-ranging collaborative effort, this library was analyzed in the Open Innovation Drug Discovery (OIDD) phenotypic assay modules publicly offered by Lilly. The results of these tests are publically available online at www.ncats.nih.gov/expertise/preclinical/pd2 and via the PubChem Database (https://pubchem.ncbi.nlm.nih.gov/) (AID 1117321). Phenotypic outcomes for numerous drugs were confirmed, including sulfonylureas as insulin secretagogues and the anti-angiogenesis actions of multikinase inhibitors sorafenib, axitinib and pazopanib. Several novel outcomes were also noted including the Wnt potentiating activities of rotenone and the antifolate class of drugs, and the anti-angiogenic activity of cetaben.

Practice and Challenges of Building a Semantic Framework for Chemogenomics Research.

Effective discovery of new drugs for complex diseases demands an integrative analysis of big data aggregated from diverse sources in chemical and biological domains, to help better understand the mechanism of drug actions and to quickly translate discovery to clinical applications. Conventional approaches are confronting critical challenges in the integration of those huge heterogeneous datasets and the rapid transformation from data to knowledge. Semantic technologies aimed at facilitating the building of a common framework that allows data sharing and utilization across applications and domains in the web, have been developed quickly and have been exhibiting a broad impact in life science. Chemogenomics serves as a bridge to connect various chemical and biological data, thus building a semantic framework for chemogenomics research could not only facilitate the development of this field but also advance the intersection among other domains. During the last few years, such framework has been developed and applied in addressing real problems. In the review, we will describe the major techniques needed to build a semantic framework, and will discuss the challenges of having such framework making a broader impact.

Electronic laboratory notebooks progress and challenges in implementation.

Electronic laboratory notebooks (ELNs) are increasingly replacing paper notebooks in life science laboratories, including those in industry, academic settings, and hospitals. ELNs offer significant advantages over paper notebooks, but adopting them in a predominantly paper-based environment is usually disruptive. The benefits of ELN increase when they are integrated with other laboratory informatics tools such as laboratory information management systems, chromatography data systems, analytical instrumentation, and scientific data management systems, but there is no well-established path for effective integration of these tools. In this article, we review and evaluate some of the approaches that have been taken thus far and also some radical new methods of integration that are emerging.