Chem2Bio2RDF is a linked open data portal that integrates data from 12 databases related to systems chemical biology. It contains over 200,000 compounds, 17,930 genes, and 646,608 compound-gene-protein associations. The portal aims to link these public data sources using semantic web technologies in order to enable exploration of how chemicals interact with biological systems. Users can browse and search the data through faceted browsers, visualizations, and SPARQL queries. Case studies demonstrate how the portal can help address scientific questions about adverse drug reactions and pathways.
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.
His Tag Protein Production and PurificationExpedeon
The study of protein regulation, structure, and function relies heavily on the expression and purification of recombinant proteins. Many recombinant proteins are expressed as fusion proteins, meaning that they contain an affinity / epitope tag. A tag is a short sequence of DNA that codes for a specific amino acid, which is frequently inserted into a target gene at the point of coding for expression at either the N or C terminal of the protein required.
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.
His Tag Protein Production and PurificationExpedeon
The study of protein regulation, structure, and function relies heavily on the expression and purification of recombinant proteins. Many recombinant proteins are expressed as fusion proteins, meaning that they contain an affinity / epitope tag. A tag is a short sequence of DNA that codes for a specific amino acid, which is frequently inserted into a target gene at the point of coding for expression at either the N or C terminal of the protein required.
Exploring Chemical and Biological Knowledge Spaces with PubChemPaul Thiessen
My presentation for the Drug Repurposing workshop at the upcoming Bio-IT World Expo.
http://www.bio-itworldexpo.com/Bio-It_Expo_Content.aspx?id=124256
Presentation abstract:
PubChem has a wealth of chemical structure and biological activity information. In conjunction with NCBI’s other resources such as PubMed and GenBank, PubChem is a vast source of information relevant to repurposing not only of established drugs but any compounds with in vivo pharmacology and/or clinical results. The challenge is how to take advantage of this knowledge. The ability to explore not only chemical similarity but relationships between diseases and disease targets has crucial value in repurposing. While focused investigations are already possible within the existing Entrez system, navigation across these linked information spaces can be difficult to do on a large scale with current tools. We are actively developing new infrastructure to support such analyses, and pursuing new methods of exploring inter- and intra-database relationships between chemicals, targets, diseases, and patents. Progress and some future direction in these areas will be presented.
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."
BITS: Overview of important biological databases beyond sequencesBITS
Module 4 Other relevant biological data sources beyond sequences
Part of training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training
Bio2RDF is an open-source project that offers a large and
connected knowledge graph of Life Science Linked Data. Each dataset is expressed using its own vocabulary, thereby hindering integration, search, query, and browse data across similar or identical types of data. With growth and content changes in source data, a manual approach to maintain mappings has proven untenable. The aim of this work is to develop a (semi)automated procedure to generate high quality mappings
between Bio2RDF and SIO using BioPortal ontologies. Our preliminary results demonstrate that our approach is promising in that it can find new mappings using a transitive closure between ontology mappings. Further development of the methodology coupled with improvements in
the ontology will offer a better-integrated view of the Life Science Linked Data
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Exploring Chemical and Biological Knowledge Spaces with PubChemPaul Thiessen
My presentation for the Drug Repurposing workshop at the upcoming Bio-IT World Expo.
http://www.bio-itworldexpo.com/Bio-It_Expo_Content.aspx?id=124256
Presentation abstract:
PubChem has a wealth of chemical structure and biological activity information. In conjunction with NCBI’s other resources such as PubMed and GenBank, PubChem is a vast source of information relevant to repurposing not only of established drugs but any compounds with in vivo pharmacology and/or clinical results. The challenge is how to take advantage of this knowledge. The ability to explore not only chemical similarity but relationships between diseases and disease targets has crucial value in repurposing. While focused investigations are already possible within the existing Entrez system, navigation across these linked information spaces can be difficult to do on a large scale with current tools. We are actively developing new infrastructure to support such analyses, and pursuing new methods of exploring inter- and intra-database relationships between chemicals, targets, diseases, and patents. Progress and some future direction in these areas will be presented.
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."
BITS: Overview of important biological databases beyond sequencesBITS
Module 4 Other relevant biological data sources beyond sequences
Part of training session "Basic Bioinformatics concepts, databases and tools" - http://www.bits.vib.be/training
Bio2RDF is an open-source project that offers a large and
connected knowledge graph of Life Science Linked Data. Each dataset is expressed using its own vocabulary, thereby hindering integration, search, query, and browse data across similar or identical types of data. With growth and content changes in source data, a manual approach to maintain mappings has proven untenable. The aim of this work is to develop a (semi)automated procedure to generate high quality mappings
between Bio2RDF and SIO using BioPortal ontologies. Our preliminary results demonstrate that our approach is promising in that it can find new mappings using a transitive closure between ontology mappings. Further development of the methodology coupled with improvements in
the ontology will offer a better-integrated view of the Life Science Linked Data
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
The French Revolution, which began in 1789, was a period of radical social and political upheaval in France. It marked the decline of absolute monarchies, the rise of secular and democratic republics, and the eventual rise of Napoleon Bonaparte. This revolutionary period is crucial in understanding the transition from feudalism to modernity in Europe.
For more information, visit-www.vavaclasses.com
Honest Reviews of Tim Han LMA Course Program.pptxtimhan337
Personal development courses are widely available today, with each one promising life-changing outcomes. Tim Han’s Life Mastery Achievers (LMA) Course has drawn a lot of interest. In addition to offering my frank assessment of Success Insider’s LMA Course, this piece examines the course’s effects via a variety of Tim Han LMA course reviews and Success Insider comments.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
1.4 modern child centered education - mahatma gandhi-2.pptx
Chem2bio2rdf portal
1. CHEM2BIO2RDF:
A LINKED OPEN DATA PORTAL FOR
SYSTEMS CHEMICAL BIOLOGY
Bin Chen, Ying Ding, Huijun Wang, David Wild, Xiao Dong,
Yuyin Sun, Qian Zhu, Madhuvanthi Sankaranarayanan
Indiana University at Bloomington
2. Chemogenomics
PPI Disease
Compound Protein Metabolic Pathway Side effect
Drug Gene Gene Regulatory Toxicity
Chemical Biology Systems Phenotype
interacting mapping
What’s Systems Chemical Biology
3. All the public data are scattered around the web…
MATADOR
4. LODD
Bio2RDF
(Drug/Chemical Data)
(biological data)
Chem2Bio2RDF
(chemogenomics---how chemical interact with biological data)
5. Linked Open Data (LOD)
Bio2RDF
LODD
Linked Life Data
Chem2Bio2RDF
6. Workflow for RDF conversion
XML
Ontology
D2R
CSV Download Scripts Mapping Dumping Virtuoso
Relational D2R
Local Triple
DB server
copy Store
TXT
Publishing
DB
…
External Sources
7. We are focusing on how chemical
interacts with biological data
12 databases
204, 981 compounds
17, 930 genes
646, 608 associations
Caveat: Not all binding data!
MATADOR
8. Literature based Systems Chemical
Biology
Covering 1865-2009
18,502,916 PubMed/Medline
literature records!
10. Chem2Bio2RDF data
Other data venders
compound
protein/gene
chemogenomics
literature
others
Node represents each database colored by its RDF vender; Directed edge shows
Over 110 million triples! the linkage from one dataset to another dataset, colored by the linkage type.
E.g,., the type compound includes CID, CAS, ChEBI, DBID and so on. The size of
Chem2Bio2RDF Datasets nodes and the width of edges are dependent on the # of triples and # of
linkages respectively.
11. Dereferenable URI
PlotViz: Visualization
Bio2RDF Browsing
Cytoscape Plugin
Virtuoso
Triple store
Chem2Bio2RDF
Linked Path Generation and Ranking
LODD
uniprot
Others
SPARQL ENDPOINTS Third party tools
15. Answer scientific questions
Give me all information about this compound
Give me all information about this target
Find chemical associated genes
Find gene associated chemicals
Find disease associated chemicals
Find side effect associated chemicals
Find all the drug-like compounds in PubChem BioAssay that
share at least two targets with a drug in DrugBank
Link KEGG / Reactome Pathways and PubChem to identify
potential multiple pathway inhibitors for MAPK
More in http://chem2bio2rdf.wikispaces.com/multiple+sources
17. 1. Scientific Question
Drugs that cause similar adverse side effects often
have totally different chemical structures
Cholestasis, Bile salt transporters in liver
18. 2. hypothesis
drug targets might function in the same pathway
19. 3. Methods
find KEGG pathways containing
at least two of the targets
associated with a given side
Path finding and visualization effect (i.e. hepatomegaly)
PREFIX chem2bio: <http://localhost:2020/vocab/resource/>
SELECT ?pathway_id (count(?pathway_id) as ?count)
WHERE {
SPARQL
?compound chem2bio:sider_side_effect ?side_effect .
?compound chem2bio:sider_cid ?dbid .
?targetid chem2bio: DrugBankTarget_dbid ?dbid .
?targetid chem2bio: DrugBankTarget_swissport_id ?UniProt_id . ?pathwayid
chem2bio:KEGG_pathway _gene_keggid ?UniProt_id .
?pathwayid chem2bio:KEGG_pathway _pathway_id ?pathway_id .
FILTER regex(?side_effect,"hepatomegaly","i") .
} GROUP BY ?pathway_id ORDER BY ?count DESC;
20. 4. results
Olanzapin
Doxazosin Isoflurane Ziprasidone Risperidone Clozapine
Drug e
GABRA GLRA ADRA1
Target PTGS2 PTGS1 GRIA1 HRH1 HTR1A HTR2A ADRA1B ADRB1 DRD2 DRD1
1 1 A
Pathwa Arachidonic VEGF Neuroactive Calcium
acid signaling ligand-receptor Small cell Pathways in signaling Gap
y
metabolism pathway interaction lung cancer cancer pathway Junction
Side Hepatic Hepatomegal
Effect Hepatitis
Necrosis y
hepatomegaly & Gap Junction?
21. 5. validation
PREFIX medline: <http://chem2bio2rdf.org/medline/resource/>
PREFIX kegg: <http://chem2bio2rdf.org/kegg/resource/>
PREFIX sider: <http://chem2bio2rdf.org/sider/resource/>
select *
from <http://chem2bio2rdf.org/medline>
from <http://chem2bio2rdf.org/kegg>
from <http://chem2bio2rdf.org/sider>
where
{
?kegg_id kegg:Pathway_name ?pathway_name . FILTER
regex(?pathway_name,"gap junction","i") .
?pmid medline:pathway ?kegg_id .
?pmid medline:side_effect ?sider .
?sider sider:side_effect ?side_effect . FILTER
regex(?side_effect,"Hepatomegaly","i") .
}
Literature based validation
Retrieve literatures talking about hepatomegaly & Gap Junction
22. Summary
Chem2Bio2RDF portal attempts to collect and link
all public data related to Systems Chemical Biology
Chem2Bio2RDF offer various tools to browse, search
and explore the data source
Case studies demonstrate that it could serve as an
useful portal in drug discovery