The collaboration enables researchers to identify drug targets and bioactive compounds via pathway analysis and retrieve comprehensive information on their synthesis, biological effects and commercial availability without having to re-query for it.
"For the first time, biologists will be able to quickly review cheminformatics data of small molecules involved in biological pathways, and chemists will be able to view molecular pathway information related to their lead compounds."
Towards semantic systems chemical biology Bin Chen
introduce a semantic framework for studying systems chemical biology / systems pharmacology, in which three major projects (Chem2Bio2RDF, Chem2Bio2OWL, SLAP (semantic link association prediction) are covered.
Big Data and the Health domain (vis-a-vis the respective H2020 Societal Challenge) - Opportunities, Challenges and Requirements. As presented and discussed in the public launch of the BigDataEurope project.
This is a presentation I gave at the FDA on December 1st 2009 in Wahington DC as part of a symposium involving PubChem, ChemIDPLus, PillBox, DailyMed and other related systems. The focus was, as usual, on the quality of data online and how to clean up the information and with a specific focus on the quality of data on the FDA's DailyMed and our efforts to apply semantic markup to the DailyMed articles
Towards semantic systems chemical biology Bin Chen
introduce a semantic framework for studying systems chemical biology / systems pharmacology, in which three major projects (Chem2Bio2RDF, Chem2Bio2OWL, SLAP (semantic link association prediction) are covered.
Big Data and the Health domain (vis-a-vis the respective H2020 Societal Challenge) - Opportunities, Challenges and Requirements. As presented and discussed in the public launch of the BigDataEurope project.
This is a presentation I gave at the FDA on December 1st 2009 in Wahington DC as part of a symposium involving PubChem, ChemIDPLus, PillBox, DailyMed and other related systems. The focus was, as usual, on the quality of data online and how to clean up the information and with a specific focus on the quality of data on the FDA's DailyMed and our efforts to apply semantic markup to the DailyMed articles
The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
This presentation describes the work of the Global Alliance for Genomics and Health, and its members, to develop standards and technologies to make genomics and clinical data more findable, accessible, and useful.
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of well over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.
Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities is given.
Metabolite Set Enrichment Analysis (ChemRICH)Dinesh Barupal
Metabolomics answers a fundamental question in biology: How does metabolism respond to genetic, environmental or phenotypic perturbations? Combining several metabolomics assays can yield datasets for more than 800 structurally identified metabolites. However, biological interpretations of metabolic regulation in these datasets are hindered by inherent limits of pathway enrichment statistics. We have developed ChemRICH, a statistical enrichment approach that is based on chemical similarity rather than sparse biochemical knowledge annotations. ChemRICH utilizes structure similarity and chemical ontologies to map all known metabolites and name metabolic modules. Unlike pathway mapping, this strategy yields study-specific, non-overlapping sets of all identified metabolites. Subsequent enrichment statistics is superior to pathway enrichments because ChemRICH sets have a self-contained size where p-values do not rely on the size of a background database. We demonstrate ChemRICH’s efficiency on a public metabolomics data set discerning the development of type 1 diabetes in a non-obese diabetic mouse model. ChemRICH is available at www.chemrich.fiehnlab.ucdavis.edu
ANALYSIS OF PROTEIN MICROARRAY DATA USING DATA MININGijbbjournal
Latest progress in biology, medical science, bioinformatics, and biotechnology has become important and
tremendous amounts of biodata that demands in-depth analysis. On the other hand, recent progress in data
mining research has led to the development of numerous efficient and scalable methods for mining
interesting patterns in large databases. This paper bridge the two fields, data mining and bioinformatics
for successful mining of biological data. Microarrays constitute a new platform which allows the discovery
and characterization of proteins.
Before synthetic chemists replicate reactions or create compounds, they must determine whether the materials or precursors they need are already available - or if they must be synthesized.
"Data sources on DiscoveryGate are indexed. This allows synthetic chemists to quickly determine whether a chosen synthesis is cost-justified or prohibitive. Access to primary literature and associated Material Safety Data Sheets (MSDS) provides information on determining factors such as yield and safety."
The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
This presentation describes the work of the Global Alliance for Genomics and Health, and its members, to develop standards and technologies to make genomics and clinical data more findable, accessible, and useful.
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of well over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.
Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities is given.
Metabolite Set Enrichment Analysis (ChemRICH)Dinesh Barupal
Metabolomics answers a fundamental question in biology: How does metabolism respond to genetic, environmental or phenotypic perturbations? Combining several metabolomics assays can yield datasets for more than 800 structurally identified metabolites. However, biological interpretations of metabolic regulation in these datasets are hindered by inherent limits of pathway enrichment statistics. We have developed ChemRICH, a statistical enrichment approach that is based on chemical similarity rather than sparse biochemical knowledge annotations. ChemRICH utilizes structure similarity and chemical ontologies to map all known metabolites and name metabolic modules. Unlike pathway mapping, this strategy yields study-specific, non-overlapping sets of all identified metabolites. Subsequent enrichment statistics is superior to pathway enrichments because ChemRICH sets have a self-contained size where p-values do not rely on the size of a background database. We demonstrate ChemRICH’s efficiency on a public metabolomics data set discerning the development of type 1 diabetes in a non-obese diabetic mouse model. ChemRICH is available at www.chemrich.fiehnlab.ucdavis.edu
ANALYSIS OF PROTEIN MICROARRAY DATA USING DATA MININGijbbjournal
Latest progress in biology, medical science, bioinformatics, and biotechnology has become important and
tremendous amounts of biodata that demands in-depth analysis. On the other hand, recent progress in data
mining research has led to the development of numerous efficient and scalable methods for mining
interesting patterns in large databases. This paper bridge the two fields, data mining and bioinformatics
for successful mining of biological data. Microarrays constitute a new platform which allows the discovery
and characterization of proteins.
Before synthetic chemists replicate reactions or create compounds, they must determine whether the materials or precursors they need are already available - or if they must be synthesized.
"Data sources on DiscoveryGate are indexed. This allows synthetic chemists to quickly determine whether a chosen synthesis is cost-justified or prohibitive. Access to primary literature and associated Material Safety Data Sheets (MSDS) provides information on determining factors such as yield and safety."
Presented by Richard Kidd at "The Future Information Needs of Pharmaceutical & Medicinal Chemistry", Monday 28 November 2011 at The Linnean Society, Burlington Square, London run by the RSC CICAG group.
Web-based technologies coupled with a drive for improved communication between scientists have resulted in the proliferation of scientific opinion, data and knowledge at an ever-increasing rate. The increasing array of chemistry-related computer-based resources now available provides chemists with a direct path to the discovery of information, once previously accessed via library services and limited to commercial and costly resources. We propose that preclinical absorption, distribution, metabolism, excretion and toxicity data as well as pharmacokinetic properties from studies published in the literature (which use animal or human tissues in vitro or from in vivo studies) are precompetitive in nature and should be freely available on the web. This could be made possible by curating the literature and patents, data donations from pharmaceutical companies and by expanding the currently freely available ChemSpider database of over 21 million molecules with physicochemical properties. This will require linkage to PubMed, PubChem and Wikipedia as well as other frequently used public databases that are currently used, mining the full text publications to extract the pertinent experimental data. These data will need to be extracted using automated and manual methods, cleaned and then published to the ChemSpider or other database such that it will be freely available to the biomedical research and clinical communities. The value of the data being accessible will improve development of drug molecules with good ADME/Tox properties, facilitate computational model building for these properties and enable researchers to not repeat the failures of past drug discovery studies.
This is a presentation given at the Opal Events meeting ""Drug Discovery Partnerships: Filling the Pipeline". I was speaking in a session with Jean-Claude Bradley regarding "Pre-competitive Collaboration: Sharing Data to Increase Predictability". This presentation discussed some of the work we are doing on Open PHACTS. My thanks especially to Carole Goble, Lee Harland and Sean Ekins for their comments.
Computer-Aided Drug Designing (CADD) is a specialized discipline that uses computational methods to simulate drug-receptor interactions
CADD methods are heavily dependent on bioinformatics tools, applications, and databases
The internet continues to offer increased access to chemistry data that may be of value to scientists interested in populating systems containing reference toxicology data as well as to provide data for the development of predictive models. This presentation will give an overview of some of the various sources of data available via the internet, provide an overview of some of the challenges associated with gathering high-quality data and discuss methods by which to mesh together disparate data sources.
Slides to be presented at a webinar arranged by Metasolution as part of a Vinnova project http://metasolutions.se/2014/03/webbinarium-med-kerstin-forsberg-om-lankade-data-i-lakemedelsforskningen/
There are many characteristics of biological data. All these characteristics make the management of biological information a particularly challenging problem. Here mainly we will focus on characteristics of biological information and multidisciplinary field called bioinformatics. Bioinformatics, now a days has emerged with graduate degree programs in several universities.
As a leader in Life Sciences cloud technology, Oracle is trusted globally by professionals in large and emerging companies engaged in clinical research and pharmacovigilance. With over 20 years’ experience, we are committed to supporting clinical development, delivering innovation to accelerate advancements, and empowering the industry to improve patient outcomes.
A unified platform providing functionality based on role is a logical progression in eClinical technology development, with the majority of sponsors/CROs preferring and supporting this evolution.
Design comp (comparable) for Blog page on insidetrack.com showing how page display changes due to the responsive design of the site on PC, Tablet and Smartphone.
Connecting with confidence in healthcare. Healthcare brochure on Unified Communications solution. Healthcare organizations can strengthen patient communications while enabling cross-discipline collaboration.
The amount and complexity of information acquired and investigated during lead discovery and optimization often creates daunting information bottlenecks for researchers.
"The retrosynthetic scheme display enables chemists to quickly and efficiently determine the suitability of a synthetic route to target molecules. Retrosynthetic schemes also provide a behind-the-scenes search for potential starting materials from reaction records."
Ayasdi (ai-yaz-dee), a Silicon Valley start-up, has created technology that may prove to redefine an entire industry. Ayasdi provides a highly differentiated platform for data analysis based on the concept of Topological Data Analysis, first documented in the 1700’s – a platform that has the potential to shift the direction of future technology development. This case study briefly explores the “Big Data” industry as it is today, and the future implications that Ayasdi may have on the industry; including the strategic challenges Ayasdi has in positioning themselves as a contender and prospective leader within the “Big Data” and Enterprise Technology market segments.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
ISI 2024: Application Form (Extended), Exam Date (Out), EligibilitySciAstra
The Indian Statistical Institute (ISI) has extended its application deadline for 2024 admissions to April 2. Known for its excellence in statistics and related fields, ISI offers a range of programs from Bachelor's to Junior Research Fellowships. The admission test is scheduled for May 12, 2024. Eligibility varies by program, generally requiring a background in Mathematics and English for undergraduate courses and specific degrees for postgraduate and research positions. Application fees are ₹1500 for male general category applicants and ₹1000 for females. Applications are open to Indian and OCI candidates.
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
3D Hybrid PIC simulation of the plasma expansion (ISSS-14)
Collaboration with GeneGo provides seamless access to compound databases, patents, literature and biological pathways
1. lsevier MDL and GeneGo have
linked databases to make it easier
and quicker for researchers to
access more information without repeating
searches in multiple diverse platforms. The
GeneGo databases for systems biology
and pathway analysis (MetaCore™
and
MetaDrug™
) are now linked with the
synthesis, sourcing and bioactivity data-
bases on the DiscoveryGate®
platform.
MetaCore is a unique, curated database
of human protein-protein and protein-DNA
interactions, transcription factors, signaling
and metabolic pathways and the effects
of bioactive molecules. MetaDrug is a
systems pharmacology platform that
predicts human drug metabolism, potential
toxicities and mode of action for novel
small molecules.
The collaboration enables researchers
to identify drug targets and bioactive
compounds via pathway analysis and
retrieve comprehensive information on
their synthesis, biological effects and
commercial availability without having
to re-query for it.
“The integration of MDL databases
with GeneGo’s pathways information
systems enables scientists to bridge the
gap between cell biology and medicinal
chemistry,” says Steve Young, Director
of MDL Content Strategy. “For the first
time, biologists will be able to quickly
review cheminformatics data of small
molecules involved in biological pathways,
and chemists will be able to view molecular
pathway information related to their
lead compounds.”
“Lately, a number of customers
approached us with requests for functional
analysis of the effects of drug-like com-
pounds rather than genomic data,” says
Julie Bryant, VP Business Development
at GeneGo. “Although pathways and
network analysis of bioactive compounds
is a common practice in MetaCore, we
partnered with Elsevier MDL for in-depth
coverage of literature- and patent-derived
information relevant for compounds.
We are very pleased to be working with
Elsevier MDL, the market leader in
medicinal chemistry factual databases.
Integration with the Elsevier MDL chemistry
space opens up new applications for
our products in medicinal chemistry,
including high-throughput and high-
content screening, hit selection and
validation, lead development programs
and chemogenomics.”
Reprint from Molecular Connection Vol 24 No 4 2006
Collaboration with GeneGo provides
seamless access to compound databases,
patents, literature and biological pathways
GeneGo develops systems biology technology for life
sciences research. The original computational platform
allows an integration and expert analysis of different
kinds of experimental data (mRNA expression,
proteomics, metabolomics, siRNA and other phenotypic
data) and relevant bioactive chemistry (metabolites, drugs, other xenobiotics) within
the framework of curated biological pathways and networks. GeneGo’s flagship
product, MetaCore, assists pharmaceutical scientists in the areas of target selection
and validation, identification of biomarkers for disease states and toxicology. MetaDrug
is designed for prediction of human metabolism, toxicity and biological effects for
novel small molecules compounds. MetaBase™
represents the knowledge base
for MetaCore. For more information about GeneGo products and services, please
visit www.genego.com.
About GeneGo
“For the first time, biologists will be able to quickly
review cheminformatics data of small molecules
involved in biological pathways, and chemists will be
able to view molecular pathway information
related to their lead compounds.”
E
2. Reprint from Molecular Connection Vol 24 No 4 2006
You want to study related pharmaco-
logical information (e.g., adverse effects,
toxicity, dose response curves, primary
literature, etc.) on Celecoxib, a known
COX-2 inhibitor.
In GeneGo you conduct a signaling
networks search on Celecoxib which
builds a network mapping the relation-
ship between this compound and
targets/receptors.
Figure 1: The Celecoxib molecule is shown in the network diagram (purple hexagon, circled).
Double-click on the Celecoxib purple
hexagon to open the ‘Chemical compound
details’ display.
The default search type when transferring
a structure to DiscoveryGate is automatic
search. The system looks for records that
match the query using the following
search types in this order: exact match,
include isomers, include tautomers, include
salts, substructure, similarity (90%) and
similarity (70%), until at least one hit is
found. Each search is somewhat more
general than the preceding search.
Select substructure as the search
method to receive all substances that
contain the Celecoxib core structure and
then click on Search in DiscoveryGate
to transfer this structure to the MDL®
Compound Index (license to DiscoveryGate
required).
In addition to target information from
MetaCore you get pharmacology, safety,
toxicity, adverse effort and metabolism
data, as well as commercial availability
and preparation data via DiscoveryGate.
Select Details on the Celecoxib
record to see all related records available
via the Compound Index.
Figure 2: Celecoxib compound details. A reaction in GeneGo nomenclature is equivalent to a
metabolic transformation in MDL databases.
1
2
Figure 3: The ‘Grid View’ (background) allows you to quickly see all related structures containing
the Celecoxib core structure. The ‘Properties View’ (foreground) shows related records in a
properties context.
3
1
2
The integration of MDL
databases with GeneGo’s
pathways information
systems bridges the gap
between cell biology and
medicinal chemistry.
3. Reprint from Molecular Connection Vol 24 No 4 2006
Figure 4: DiscoveryGate provides “Also found in” links at the top of each record offering
immediate connections to relevant information on the same compound in other data sources.
45
Figure 5: xPharm and PharmaPendium record displays for Celecoxib (xPharm and PharmaPendium
licenses required).
Figure 6: Information in PubChem is categorized based on the Medical Subject Heading
(MeSH) indexing schema.
6
This record for Celecoxib includes direct
links to the GeneGo databases, that is,
bidirectional linking is enabled (MetaCore
and/or MetaData licenses required).
Click on xPharm®
and PharmaPendium™
in the ‘Also found in’ links to access a
wealth of pharmacological and adverse
effects information on Celecoxib.
Click on PubChem in the ‘Also found
in’ links to access bioassay data.
Select PubMed via MeSH to access
associated biological and pharmacological
effect information from the corresponding
primary literature.
DiscoveryGate and the MDL®
Compound Index
The online DiscoveryGate platform
(www.discoverygate.com) provides
access to integrated scientific con-
tent from databases, journal articles,
patent publications and reference
works from information providers
including Elsevier, Thomson-Derwent,
FIZ CHEMIE, the USFDA, Prous
Science and Thieme.
With the addition of chemical
structures from the GeneGo data-
bases, MetaCore and MetaDrug,
the MDL Compound Index (the
master list of substances included
in DiscoveryGate data sources)
now exceeds 16.5 million unique
chemical structures. Altogether, more
than 22 million unique structures are
accessible via DiscoveryGate.
4
5
6
The collaboration with
GeneGo expands the network
by enabling researchers to
link from molecules in
GeneGo’s biological
pathways to DiscoveryGate
to find related information.