Navigating links between structures and papers:
PubMed-to-PubChem connectivity between the IUPHAR/BPS Guide to PHARMACOLOGY and British Journal of Pharmacology
A poster presented at Pharmacology 2017, London, December 2017
Poster for World Congres of Pharmacology 2018, Kyoto
Introduction: The pharmacological literature and patents connect compound structures to their bioactivity. However, entombing these relationships for millions of compounds among millions of PDFs is acknowledged as massively problematic. The situation is ameliorated by resources that extract the entity and data relationships the authors and inventors put “in” to their PDFs back “out” into structured database records. The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) has been doing this by stringent curation of ligands and their quantitative activity against protein targets [1]. Our citations are submitted to PubChem (PC), who then link to PubMed (PM) [2]. This study presents an overview of this connectivity.
Methods: For GtoPdb entries in PC Substance we used the PC interface to count our submitted PM links. This gives the PC > PM mapping counts from which we analysed the PM links. We then performed reciprocal analyses (i.e. PM > PC) by selecting PM sets. We then compared two journals by counting structure links by year and source.
Results: From 8988 GtoPdb-submitted ligand substances in PC (release 2017.5), 7309 are linked to 8980 PM entries. Of the 7309 there are 5632 links to chemical structures in PC the rest being antibodies and larger peptides. From the 8980 PMIDs, the Journal of Medicinal Chemistry (JMC) accounted for 1003 as our most frequently cited primary source of structure-to-activity mappings. For the British Journal of Pharmacology (BJP) most of the 345 cross-references were development compounds. Further analysis showed that from 2014 to 2017 the BJP to PC links of ~ 30 structures per year are mostly from GtoPdb and the Comparative Toxicology Database. However, going back to 2010-12, this increased to 500-800 connections, mainly derived from the IBM automated chemical extraction from abstracts. A similar pattern was observed for JMC.
Conclusion: Navigation between documents and databases is an essential competence for pharmacologists and drug discovery but the NCBI Entrez system is daunting. GtoPdb is a major contributor of high-quality links and provides a first-stop to guide users into the PC/PM systems. However, our results indicated potentially serious specificity issues with automated chemistry-to-journal linking from non-GtoPdb sources.
References: [1] Harding et al. (2018). Nucl. Acids Res. 45 (Database Issue), doi: 10.1093/nar/gkx1121.
A Novel Data Extraction and Alignment Method for Web DatabasesIJMER
International Journal of Modern Engineering Research (IJMER) is Peer reviewed, online Journal. It serves as an international archival forum of scholarly research related to engineering and science education.
International Journal of Modern Engineering Research (IJMER) covers all the fields of engineering and science: Electrical Engineering, Mechanical Engineering, Civil Engineering, Chemical Engineering, Computer Engineering, Agricultural Engineering, Aerospace Engineering, Thermodynamics, Structural Engineering, Control Engineering, Robotics, Mechatronics, Fluid Mechanics, Nanotechnology, Simulators, Web-based Learning, Remote Laboratories, Engineering Design Methods, Education Research, Students' Satisfaction and Motivation, Global Projects, and Assessment…. And many more.
The document summarizes recent updates to the IUPHAR/BPS Guide to PHARMACOLOGY database. It describes new features including expanded target coverage with over 1,700 drug targets and 1,100 related proteins. A new Pharmacology Search Tool allows users to upload protein lists and find associated ligands. The database also now connects immunopharmacology by associating targets with immune processes, cell types, and diseases. Additionally, the guide describes collaborations to include antimalarial compound data and develop an IUPHAR/MMV Guide to Malaria Pharmacology.
The document provides an overview and progress report on database activities from April 2018 - March 2019. Key points include:
- Publications in peer-reviewed journals on the database and new immunopharmacology guide.
- Engagement through conferences, social media, and interactions with users seeking to improve the database.
- Ongoing development of the database interface and content, including expansion to new therapeutic areas.
- Statistics on usage, file downloads, and web service calls that show increasing interaction over time.
A survey on Design and Implementation of Clever Crawler Based On DUST RemovalIJSRD
Now days, World Wide Web has become a popular medium to search information, business, trading and so on. A well know problem face by web crawler is the existence of large fraction of distinct URL that correspond to page with duplicate or nearby duplicate contents. In fact as estimated about 29% of web page are duplicates. Such URL commonly named as dust represent an important problem in search engines. To deal with this problem, the first efforts is focus on comparing document content to detect and remove duplicate document without fetching their contents .To accomplish this, the proposed methods learn normalization rules to transform all duplicate URLs into the same canonical form. A challenging aspect of this strategy is deriving a set of general and precise rules. The new approach to detect and eliminate redundant content is DUSTER .When crawling the web duster take advantage of a multi sequence alignment strategy to learn rewriting rules able to transform to other URL which likely to have same content . Alignment strategy that can lead to reduction of 54% larger in the number of duplicate URL.
There is increasing interest in the environmental impact of per- and polyfluoroalkyl substances (PFAS) chemicals and the aggregation of related data provides both agency and public access to support research. The US-EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~875,000 chemical substances, including thousands of PFAS chemicals. The dashboard provides access to a wide array of experimental and predicted physicochemical properties, in vitro bioactivity and in vivo toxicity data, product use information and integrated linkages to a growing list of literature, toxicology, and analytical chemistry websites. The assembly of data has required hundreds of hours of manual curation and data checking to deliver a number of segregated lists of PFAS chemicals. Experimental data extracted from literature articles has allowed the optimization of QSAR models for the prediction of properties such as logP (octanol-water partition) and aqueous solubility. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models being developed for these chemicals. Our progress in the measurement and analysis of bioactivity data for PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
Chemicalize.org: User-Selected PubChem Source of Structures from TextChris Southan
Chemicalize.org is a web application that extracts chemical structures from text sources like patents and Wikipedia pages. It has generated a searchable database of over 300,000 unique structures from user inputs. These structures are deposited in PubChem and link back to their source pages on Chemicalize.org. Around 70% of structures come from patent texts, with the rest from sources like Wikipedia. The structures extracted by Chemicalize.org show drug-like properties, with 71% following the Lipinski rule of five. They provide a unique source of compounds in PubChem derived from active user selection of documents.
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an open, expert-driven database that contains information on over 1,700 pharmacological targets and the substances that act on them. The database provides overviews and detailed information on targets that is manually curated from literature and reviewed by experts. It aims to cover human drug targets and potential future therapeutic targets. New features of the database include search tools to find targets and ligands, information on diseases associated with targets and ligands, organization of ligand families, and comparison of ligand activity across species. The database content is available to download in various formats and its interoperability has been increased through developing an RDF version and submitting data to other sources
Poster for World Congres of Pharmacology 2018, Kyoto
Introduction: The pharmacological literature and patents connect compound structures to their bioactivity. However, entombing these relationships for millions of compounds among millions of PDFs is acknowledged as massively problematic. The situation is ameliorated by resources that extract the entity and data relationships the authors and inventors put “in” to their PDFs back “out” into structured database records. The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) has been doing this by stringent curation of ligands and their quantitative activity against protein targets [1]. Our citations are submitted to PubChem (PC), who then link to PubMed (PM) [2]. This study presents an overview of this connectivity.
Methods: For GtoPdb entries in PC Substance we used the PC interface to count our submitted PM links. This gives the PC > PM mapping counts from which we analysed the PM links. We then performed reciprocal analyses (i.e. PM > PC) by selecting PM sets. We then compared two journals by counting structure links by year and source.
Results: From 8988 GtoPdb-submitted ligand substances in PC (release 2017.5), 7309 are linked to 8980 PM entries. Of the 7309 there are 5632 links to chemical structures in PC the rest being antibodies and larger peptides. From the 8980 PMIDs, the Journal of Medicinal Chemistry (JMC) accounted for 1003 as our most frequently cited primary source of structure-to-activity mappings. For the British Journal of Pharmacology (BJP) most of the 345 cross-references were development compounds. Further analysis showed that from 2014 to 2017 the BJP to PC links of ~ 30 structures per year are mostly from GtoPdb and the Comparative Toxicology Database. However, going back to 2010-12, this increased to 500-800 connections, mainly derived from the IBM automated chemical extraction from abstracts. A similar pattern was observed for JMC.
Conclusion: Navigation between documents and databases is an essential competence for pharmacologists and drug discovery but the NCBI Entrez system is daunting. GtoPdb is a major contributor of high-quality links and provides a first-stop to guide users into the PC/PM systems. However, our results indicated potentially serious specificity issues with automated chemistry-to-journal linking from non-GtoPdb sources.
References: [1] Harding et al. (2018). Nucl. Acids Res. 45 (Database Issue), doi: 10.1093/nar/gkx1121.
A Novel Data Extraction and Alignment Method for Web DatabasesIJMER
International Journal of Modern Engineering Research (IJMER) is Peer reviewed, online Journal. It serves as an international archival forum of scholarly research related to engineering and science education.
International Journal of Modern Engineering Research (IJMER) covers all the fields of engineering and science: Electrical Engineering, Mechanical Engineering, Civil Engineering, Chemical Engineering, Computer Engineering, Agricultural Engineering, Aerospace Engineering, Thermodynamics, Structural Engineering, Control Engineering, Robotics, Mechatronics, Fluid Mechanics, Nanotechnology, Simulators, Web-based Learning, Remote Laboratories, Engineering Design Methods, Education Research, Students' Satisfaction and Motivation, Global Projects, and Assessment…. And many more.
The document summarizes recent updates to the IUPHAR/BPS Guide to PHARMACOLOGY database. It describes new features including expanded target coverage with over 1,700 drug targets and 1,100 related proteins. A new Pharmacology Search Tool allows users to upload protein lists and find associated ligands. The database also now connects immunopharmacology by associating targets with immune processes, cell types, and diseases. Additionally, the guide describes collaborations to include antimalarial compound data and develop an IUPHAR/MMV Guide to Malaria Pharmacology.
The document provides an overview and progress report on database activities from April 2018 - March 2019. Key points include:
- Publications in peer-reviewed journals on the database and new immunopharmacology guide.
- Engagement through conferences, social media, and interactions with users seeking to improve the database.
- Ongoing development of the database interface and content, including expansion to new therapeutic areas.
- Statistics on usage, file downloads, and web service calls that show increasing interaction over time.
A survey on Design and Implementation of Clever Crawler Based On DUST RemovalIJSRD
Now days, World Wide Web has become a popular medium to search information, business, trading and so on. A well know problem face by web crawler is the existence of large fraction of distinct URL that correspond to page with duplicate or nearby duplicate contents. In fact as estimated about 29% of web page are duplicates. Such URL commonly named as dust represent an important problem in search engines. To deal with this problem, the first efforts is focus on comparing document content to detect and remove duplicate document without fetching their contents .To accomplish this, the proposed methods learn normalization rules to transform all duplicate URLs into the same canonical form. A challenging aspect of this strategy is deriving a set of general and precise rules. The new approach to detect and eliminate redundant content is DUSTER .When crawling the web duster take advantage of a multi sequence alignment strategy to learn rewriting rules able to transform to other URL which likely to have same content . Alignment strategy that can lead to reduction of 54% larger in the number of duplicate URL.
There is increasing interest in the environmental impact of per- and polyfluoroalkyl substances (PFAS) chemicals and the aggregation of related data provides both agency and public access to support research. The US-EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) is a publicly accessible website providing access to data for ~875,000 chemical substances, including thousands of PFAS chemicals. The dashboard provides access to a wide array of experimental and predicted physicochemical properties, in vitro bioactivity and in vivo toxicity data, product use information and integrated linkages to a growing list of literature, toxicology, and analytical chemistry websites. The assembly of data has required hundreds of hours of manual curation and data checking to deliver a number of segregated lists of PFAS chemicals. Experimental data extracted from literature articles has allowed the optimization of QSAR models for the prediction of properties such as logP (octanol-water partition) and aqueous solubility. This presentation will provide an overview of the dashboard, the ongoing expansion of the PFAS chemical library, with associated categorization, and new physicochemical property and environmental fate and transport QSAR prediction models being developed for these chemicals. Our progress in the measurement and analysis of bioactivity data for PFAS chemicals will also be reviewed. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.
Chemicalize.org: User-Selected PubChem Source of Structures from TextChris Southan
Chemicalize.org is a web application that extracts chemical structures from text sources like patents and Wikipedia pages. It has generated a searchable database of over 300,000 unique structures from user inputs. These structures are deposited in PubChem and link back to their source pages on Chemicalize.org. Around 70% of structures come from patent texts, with the rest from sources like Wikipedia. The structures extracted by Chemicalize.org show drug-like properties, with 71% following the Lipinski rule of five. They provide a unique source of compounds in PubChem derived from active user selection of documents.
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an open, expert-driven database that contains information on over 1,700 pharmacological targets and the substances that act on them. The database provides overviews and detailed information on targets that is manually curated from literature and reviewed by experts. It aims to cover human drug targets and potential future therapeutic targets. New features of the database include search tools to find targets and ligands, information on diseases associated with targets and ligands, organization of ligand families, and comparison of ligand activity across species. The database content is available to download in various formats and its interoperability has been increased through developing an RDF version and submitting data to other sources
GtoPdb: A resource for cell-based perturbogensChris Southan
Poster for ELRIG, Möndal, 11/12 May 2017.
This poster will also be presented at BioITWorld, Boston, May 23-25
A resource for the selection and interpretation of cell-based perturbogens: the IUPHAR/BPS Guide to PHARMACOLOGY
Christopher Southan, Elena Faccenda, Joanna L. Sharman, Adam J. Pawson, Simon D. Harding, Jamie A Davies,
Translational research requires the integration of the in vitro molecular mechanisms of action (mmoa) of small molecules, cell-based screening studies, animal models and eventual clinical trials. The International Union of Pharmacology (IUPHAR)/British Pharmacology Society (BPS) database, GtoPdb http://www.guidetopharmacology.org/ provides expert-annotated molecular interactions between endogenous receptor ligands, probes, lead compounds, clinical drugs and their protein targets. It thus provides a core set of quantitative pharmacological relationships that can be interrogated for many purposes, including those running cell-based screens, not only during result interpretation but also to identify key compounds for scoping and consolidation experiments. As described in [1] GtoPdb is populated by records extracted from pharmacology and medicinal chemistry journals, and released quarterly. Quality is ensured by curatorial stringency and our unique model of content selection based on recommendations from IUPHAR target class subcommittees of international experts collaborating with the in-house curators. The database now has over 14 000 binding values (mainly IC50, Ki or Kd) between 8000 ligands and 15000 human proteins (mainly primary but also secondary off-target interactions) representing a 7% druggable proteome. Our coverage is complementary to other sources. For example the 6565 structures we recently submitted to PubChem as CIDs, 5206 were not in DrugBank and 1535 not in ChEMBL. This includes recommended tool compounds with relatively defined mmoa (including 110 from the Structural Genomics Consortium Probe Portal). We also have 75% overlap with vendors for procurement and 80% with patent extractions that in many cases allow mapping to SAR data sets from first-filings (some of which we point to). In a cell screening context 1254 of our targets intersect with proteins in the Reactome pathway database. This is one way to select chemical peturbation points that could be detected by assay readouts. From Nov 2015 we have been funded by the Wellcome Trust to extend into immunopharmacology (within the existing database schema) that is now driving overall GtoPdb content expansion. Parties engaged in cell based assays using or could use compounds we have are encouraged to use GtoPdb, contact us for queries, possible analogue expansions and/or alert us to prospective new content. [1] Southan C et. al. (2016) Nucleic Acids Res. 44(D1):D1054-68, PMID: 26464438
PubChem for drug discovery and chemical biologyChris Southan
This document provides an overview of the PubChem database for academic drug discovery and chemical biology. It describes PubChem's large content of over 97 million compounds and 3.4 million with bioactivity results. It highlights drug-related resources in PubChem like ChEMBL and the Guide to Pharmacology. It also demonstrates several use cases, including searching structures extracted from patents, linking between papers and chemistry, and getting probes mapped into PubChem.
Scholarly Communication for Bioinformatics StudentsPhilip Bourne
Presentation made to the incoming bioinformatics and systems biology students at UCSD on how they could get involved in changing scholarly communication. Given February 28, 2011
The document provides an overview and status report of the Core Guide to PHARMACOLOGY (GtoPdb) database. It discusses recent publications from the team, compliance with new GDPR privacy regulations, website access statistics showing increased usage, new website features, and priorities for further development such as expanding disease and content coverage.
Assessing GtoPdb ligand content in PubChemChris Southan
The document discusses the content of ligands from the IUPHAR/BPS Guide to PHARMACOLOGY database (GtoPdb) that is contained within PubChem. It finds that GtoPdb ligands have extensive overlap with several other sources within PubChem, including patents, DrugBank, vendor structures, bioassays, and ChEMBL. This overlap allows users to find additional information on GtoPdb ligands from these complementary sources within PubChem.
Mail merge allows the creation of form letters, labels, and envelopes by linking a main document to a data source containing fields like names and addresses. The main document contains merge fields that are populated from the data source for each recipient. For example, a form letter's main document would contain the letter text, while the data source would have each customer's personalized details to populate the merge fields. This allows mass customization of documents without recreating each from scratch.
1-Click Docking is a simple online molecular docking tool that predicts the binding orientation of a single ligand to a single target protein. It provides a rough estimate of binding affinity and allows visualization of binding poses. The tool allows users to draw a ligand, select a target protein from prepared PDB files, and click dock to obtain results. It can help understand how modifications to a scaffold affect binding affinity and interactions with key amino acids.
This document discusses the linking between the Guide to Pharmacology (GtoP) database and other databases including PubChem and PubMed. It covers two main themes: 1) Out-links from British Pharmacology Society journals to GtoP and 2) Submissions of ligands and references from GtoP to PubChem and reciprocal linking between these databases and PubMed. Over 1,100 papers from the British Journal of Pharmacology and 284 papers from the British Journal of Clinical Pharmacology have been linked to GtoP. Reciprocal linking between the databases provides benefits for users by allowing navigation between the resources.
The document discusses how the IUPHAR/BPS Guide to Pharmacology (GtoPdb) establishes connections between journal articles, chemical structures in PubChem, and citations in PubMed. GtoPdb experts curate compounds and their molecular mechanisms of action from papers and link them with PubChem substance IDs and PubMed IDs. PubChem then links the substance IDs to the PubMed IDs, creating reciprocal connections between chemistry and literature. This allows users to navigate between the databases. The document compares GtoPdb's coverage and extraction methods to other sources that link chemistry and literature, noting both opportunities and challenges in connecting information across different database systems.
Open Acess Sources for Protein Interaction InhibitorsChris Southan
The document discusses how open-access chemical databases now enable systems biologists to map bioactive compounds between literature, patents, and databases without requiring chemical drawing expertise or expensive subscriptions. It evaluates resources like PubChem and ChEBI that can be used to identify and compare protein-protein interaction inhibitors referenced in a Nature review. For example, the compound "Nutlin-3" could be mapped between PubChem and ChEBI using accession numbers and structure representations. Some compounds still cannot be fully disambiguated, but many can now be linked to literature and patents through open resources.
Looking at chemistry - protein - papers connectivity in ELIXIRChris Southan
This is a poster for the UK ELXIR meetin in Birmingham UK, Nov 2018. It is the summary of a blog-post https://cdsouthan.blogspot.com/2018/08/an-initial-look-at-elixir-chemistry.html that asses chemistry <> protein <> papers connectivity (C-P-P) for five ELIXIR resources
The document presents a systematic literature review of research on big data analytics in supply chain management from 2011 to 2021. It analyzes the literature from both organizational and technical perspectives. From an organizational perspective, it examines the theoretical foundations and models used to explain how big data analytics improves sustainability and performance. From a technical perspective, it analyzes the types of analytics, techniques, algorithms, and features developed for supply chain functions. The review identifies gaps in the research and provides directions for future work.
The document discusses the Biomolecular Interaction Network Database (BIND), which stores information about molecular interactions, complexes, and pathways. BIND uses standards like ASN.1 and XML to specify interactions. It stores details about molecules, interactions, publications, and more. Tools like Pajek and MCODE are used to visualize and analyze the network. The database has expanded to include additional details like post-translational modifications, cellular localization, and links to other databases. Manual and automatic submission is supported.
Review on Computational Bioinformatics and Molecular Modelling Novel Tool for...ijtsrd
Advancement in science and technology has brought a remarkable change in the field of drug discovery. Earlier it was very difficult to predict the target for receptor but nowadays, it is easy and robust task to dock the target protein with ligand and binding affinity is calculated. Docking helps in the virtual screening of drug along with its hit identification. There are two approaches through which docking can be carried out, shape complementary and stimulation approach. There are many procedures involved in carrying out docking and all require different software's and algorithms. Molecular docking serves as a good platform to screen a large number of ligands and is useful in Drug-DNA studies. This review mainly focuses on the general idea of molecular docking and discusses its major applications, different types of interaction involved and types of docking. Rishabh Jain "Review on Computational Bioinformatics and Molecular Modelling: Novel Tool for Drug Discovery" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-3 | Issue-1 , December 2018, URL: http://www.ijtsrd.com/papers/ijtsrd18914.pdf
http://www.ijtsrd.com/pharmacy/pharmacoinformatics/18914/review-on-computational-bioinformatics-and-molecular-modelling-novel-tool-for-drug-discovery/rishabh-jain
Poster presented at the Elixir All-Hands Meeting in Lisbon, June 2019. Gives a broad summary of Guide to Pharmacology activities in the last year. Emphasising new tools and our extension into malaria pharmacology.
This document provides an overview of the International Union of Basic and Clinical Pharmacology Guide to Pharmacology (GtoPdb) database. It describes the database contents including over 1,700 drug targets and 9,400 ligands. The database is curated by 500 experts and provides target and ligand information for researchers. Specialized versions of the database have also been created for immunopharmacology and malaria research.
Navigating between publications and databases for drug discovery: IUPHAR/BPS ...Guide to PHARMACOLOGY
Presented by team member Joanna Sharman in April 2015 at the BPS Focused Meeting: Exploiting the new pharmacology and application to drug discovery in Edinburgh.
Reactome is a free, open-source, curated and peer-
reviewed knowledge-base of biomolecular pathways.
Its aim is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education.
Drug-to-protein mappings in the Guide to PHARMACOLOGY: Utility as a target va...Guide to PHARMACOLOGY
The Guide to Pharmacology database (GtoPdb) provides expertly curated information on drug-protein interactions and targets of approved and investigational drugs. It currently includes data on interactions between over 1400 protein targets and 7700 ligands derived from over 5000 literature references. The database covers major target classes and provides a useful resource for target validation and drug discovery. Future plans include regular updates with new target and drug data as well as potential specialty sub-portals within the database.
Sorting bioactive wheat from database chaff: Challenges of discerning correct...Guide to PHARMACOLOGY
Since 2009 the Guide to PHARMACOLOGY database (GtoPdb) team have curated 7586 ligands from papers, including approved drugs, clinical candidates , research compounds peptides and clinical antibodies (PMID 24234439). As PubChem pushes towards 70 million compound identifiers (CIDs), we have noticed the problem
of “multiplexing” during the curation of 5713 small molecules as CIDs. we encountered many representations (i.e. different CIDs) of the same pharmacological entities. Three types of variation dominate: stereochemistry, mixtures and isotopic analogues. These are known constitutive issues for chemical databases but in
recent years we observed this multiplexing was reaching
problematic proportions (i.e. more chaff), especially for clinically used drugs (i.e. proportionally less wheat)
Sorting bioactive wheat from database chaffChris Southan
Abstract
Databases of bioactive compounds are crucial for pharmacology, drug discovery and chemical genomics as public sources approach ~ 100 million records. However, in recent years this famine-to-feast presents difficulties for searching chemical structures and linked activity data, particularly for those unfamiliar with the constitutive challenges of molecular representation in silico (PMID 25415348). A key problem is entries of structural variants of “the same thing” as pharmacological entities (i.e. representational multiplexing). For example, a 2009 comparison of three database subsets of ~1200 approved drugs recorded only 807 structures in-common (PMID 20298516). In addition, published counts of approved drugs vary widely. These issues have been continually encountered by the Guide to PHARMACOLOGY database (GtoPdb) team that, since 2009, has achieved the curation of ~5500 small molecules (including approved drugs) from papers. Concomitantly, we have noticed an increase in multiplexing as PubChem pushes towards 65 million compound identifiers (CIDs). Since one of our key objectives is to affinity-map ligands to their targets, we decided to assess this multiplexing problem in order to optimise our curation rules. The results have implications for the entire bioactivity information space. We began by compiling CID sets for seven different sources within PubChem encompassing approved drugs. Initially a 7x7 pairwise comparison matrix indicated low overlap between these sources. A Venn diagram was then made from the approved drug CIDs mapped by DrugBank, Therapeutic Target Database and ChEMBL. At 749, the three-way intersect was less than 35% of the union of all CIDs covered by the sets. Strikingly, this looks worse that the 2009 study (although the sources and comparison methods were different). We will present further analyses that go some way towards explaining these results. One of these is determining “same connectivity” statistics inside PubChem as a measure of multiplexing. For DrugBank, each approved drug was related to, on average, 19 different CIDs as structural variants. Analysis of multiplexing confirmed trends we had observed during individual drug curation. This included ~ 30% stereoisomer enumerations but, surprisingly, ~70% isotopic derivatives, dominated by patent-derived virtual deuteration. We also established the ratio of submissions (SIDs) to CIDs was 78. The paradox was that, despite this high “majority vote” support for approved drug CIDs curated by DrugBank, only 55% were in the 3-way consensus (figures for the other two curated sources were similar). Analysing by year in PubChem indicated how the recent expansion of vendor and patent-extraction structures contributes to both multiplexing and the SID: CID ratio. While approved drugs are strongly impacted, associated problems, such as split activity data and deciding the “correct” structures, affect essentially all public drug discovery chem
GtoPdb: A resource for cell-based perturbogensChris Southan
Poster for ELRIG, Möndal, 11/12 May 2017.
This poster will also be presented at BioITWorld, Boston, May 23-25
A resource for the selection and interpretation of cell-based perturbogens: the IUPHAR/BPS Guide to PHARMACOLOGY
Christopher Southan, Elena Faccenda, Joanna L. Sharman, Adam J. Pawson, Simon D. Harding, Jamie A Davies,
Translational research requires the integration of the in vitro molecular mechanisms of action (mmoa) of small molecules, cell-based screening studies, animal models and eventual clinical trials. The International Union of Pharmacology (IUPHAR)/British Pharmacology Society (BPS) database, GtoPdb http://www.guidetopharmacology.org/ provides expert-annotated molecular interactions between endogenous receptor ligands, probes, lead compounds, clinical drugs and their protein targets. It thus provides a core set of quantitative pharmacological relationships that can be interrogated for many purposes, including those running cell-based screens, not only during result interpretation but also to identify key compounds for scoping and consolidation experiments. As described in [1] GtoPdb is populated by records extracted from pharmacology and medicinal chemistry journals, and released quarterly. Quality is ensured by curatorial stringency and our unique model of content selection based on recommendations from IUPHAR target class subcommittees of international experts collaborating with the in-house curators. The database now has over 14 000 binding values (mainly IC50, Ki or Kd) between 8000 ligands and 15000 human proteins (mainly primary but also secondary off-target interactions) representing a 7% druggable proteome. Our coverage is complementary to other sources. For example the 6565 structures we recently submitted to PubChem as CIDs, 5206 were not in DrugBank and 1535 not in ChEMBL. This includes recommended tool compounds with relatively defined mmoa (including 110 from the Structural Genomics Consortium Probe Portal). We also have 75% overlap with vendors for procurement and 80% with patent extractions that in many cases allow mapping to SAR data sets from first-filings (some of which we point to). In a cell screening context 1254 of our targets intersect with proteins in the Reactome pathway database. This is one way to select chemical peturbation points that could be detected by assay readouts. From Nov 2015 we have been funded by the Wellcome Trust to extend into immunopharmacology (within the existing database schema) that is now driving overall GtoPdb content expansion. Parties engaged in cell based assays using or could use compounds we have are encouraged to use GtoPdb, contact us for queries, possible analogue expansions and/or alert us to prospective new content. [1] Southan C et. al. (2016) Nucleic Acids Res. 44(D1):D1054-68, PMID: 26464438
PubChem for drug discovery and chemical biologyChris Southan
This document provides an overview of the PubChem database for academic drug discovery and chemical biology. It describes PubChem's large content of over 97 million compounds and 3.4 million with bioactivity results. It highlights drug-related resources in PubChem like ChEMBL and the Guide to Pharmacology. It also demonstrates several use cases, including searching structures extracted from patents, linking between papers and chemistry, and getting probes mapped into PubChem.
Scholarly Communication for Bioinformatics StudentsPhilip Bourne
Presentation made to the incoming bioinformatics and systems biology students at UCSD on how they could get involved in changing scholarly communication. Given February 28, 2011
The document provides an overview and status report of the Core Guide to PHARMACOLOGY (GtoPdb) database. It discusses recent publications from the team, compliance with new GDPR privacy regulations, website access statistics showing increased usage, new website features, and priorities for further development such as expanding disease and content coverage.
Assessing GtoPdb ligand content in PubChemChris Southan
The document discusses the content of ligands from the IUPHAR/BPS Guide to PHARMACOLOGY database (GtoPdb) that is contained within PubChem. It finds that GtoPdb ligands have extensive overlap with several other sources within PubChem, including patents, DrugBank, vendor structures, bioassays, and ChEMBL. This overlap allows users to find additional information on GtoPdb ligands from these complementary sources within PubChem.
Mail merge allows the creation of form letters, labels, and envelopes by linking a main document to a data source containing fields like names and addresses. The main document contains merge fields that are populated from the data source for each recipient. For example, a form letter's main document would contain the letter text, while the data source would have each customer's personalized details to populate the merge fields. This allows mass customization of documents without recreating each from scratch.
1-Click Docking is a simple online molecular docking tool that predicts the binding orientation of a single ligand to a single target protein. It provides a rough estimate of binding affinity and allows visualization of binding poses. The tool allows users to draw a ligand, select a target protein from prepared PDB files, and click dock to obtain results. It can help understand how modifications to a scaffold affect binding affinity and interactions with key amino acids.
This document discusses the linking between the Guide to Pharmacology (GtoP) database and other databases including PubChem and PubMed. It covers two main themes: 1) Out-links from British Pharmacology Society journals to GtoP and 2) Submissions of ligands and references from GtoP to PubChem and reciprocal linking between these databases and PubMed. Over 1,100 papers from the British Journal of Pharmacology and 284 papers from the British Journal of Clinical Pharmacology have been linked to GtoP. Reciprocal linking between the databases provides benefits for users by allowing navigation between the resources.
The document discusses how the IUPHAR/BPS Guide to Pharmacology (GtoPdb) establishes connections between journal articles, chemical structures in PubChem, and citations in PubMed. GtoPdb experts curate compounds and their molecular mechanisms of action from papers and link them with PubChem substance IDs and PubMed IDs. PubChem then links the substance IDs to the PubMed IDs, creating reciprocal connections between chemistry and literature. This allows users to navigate between the databases. The document compares GtoPdb's coverage and extraction methods to other sources that link chemistry and literature, noting both opportunities and challenges in connecting information across different database systems.
Open Acess Sources for Protein Interaction InhibitorsChris Southan
The document discusses how open-access chemical databases now enable systems biologists to map bioactive compounds between literature, patents, and databases without requiring chemical drawing expertise or expensive subscriptions. It evaluates resources like PubChem and ChEBI that can be used to identify and compare protein-protein interaction inhibitors referenced in a Nature review. For example, the compound "Nutlin-3" could be mapped between PubChem and ChEBI using accession numbers and structure representations. Some compounds still cannot be fully disambiguated, but many can now be linked to literature and patents through open resources.
Looking at chemistry - protein - papers connectivity in ELIXIRChris Southan
This is a poster for the UK ELXIR meetin in Birmingham UK, Nov 2018. It is the summary of a blog-post https://cdsouthan.blogspot.com/2018/08/an-initial-look-at-elixir-chemistry.html that asses chemistry <> protein <> papers connectivity (C-P-P) for five ELIXIR resources
The document presents a systematic literature review of research on big data analytics in supply chain management from 2011 to 2021. It analyzes the literature from both organizational and technical perspectives. From an organizational perspective, it examines the theoretical foundations and models used to explain how big data analytics improves sustainability and performance. From a technical perspective, it analyzes the types of analytics, techniques, algorithms, and features developed for supply chain functions. The review identifies gaps in the research and provides directions for future work.
The document discusses the Biomolecular Interaction Network Database (BIND), which stores information about molecular interactions, complexes, and pathways. BIND uses standards like ASN.1 and XML to specify interactions. It stores details about molecules, interactions, publications, and more. Tools like Pajek and MCODE are used to visualize and analyze the network. The database has expanded to include additional details like post-translational modifications, cellular localization, and links to other databases. Manual and automatic submission is supported.
Review on Computational Bioinformatics and Molecular Modelling Novel Tool for...ijtsrd
Advancement in science and technology has brought a remarkable change in the field of drug discovery. Earlier it was very difficult to predict the target for receptor but nowadays, it is easy and robust task to dock the target protein with ligand and binding affinity is calculated. Docking helps in the virtual screening of drug along with its hit identification. There are two approaches through which docking can be carried out, shape complementary and stimulation approach. There are many procedures involved in carrying out docking and all require different software's and algorithms. Molecular docking serves as a good platform to screen a large number of ligands and is useful in Drug-DNA studies. This review mainly focuses on the general idea of molecular docking and discusses its major applications, different types of interaction involved and types of docking. Rishabh Jain "Review on Computational Bioinformatics and Molecular Modelling: Novel Tool for Drug Discovery" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-3 | Issue-1 , December 2018, URL: http://www.ijtsrd.com/papers/ijtsrd18914.pdf
http://www.ijtsrd.com/pharmacy/pharmacoinformatics/18914/review-on-computational-bioinformatics-and-molecular-modelling-novel-tool-for-drug-discovery/rishabh-jain
Poster presented at the Elixir All-Hands Meeting in Lisbon, June 2019. Gives a broad summary of Guide to Pharmacology activities in the last year. Emphasising new tools and our extension into malaria pharmacology.
This document provides an overview of the International Union of Basic and Clinical Pharmacology Guide to Pharmacology (GtoPdb) database. It describes the database contents including over 1,700 drug targets and 9,400 ligands. The database is curated by 500 experts and provides target and ligand information for researchers. Specialized versions of the database have also been created for immunopharmacology and malaria research.
Navigating between publications and databases for drug discovery: IUPHAR/BPS ...Guide to PHARMACOLOGY
Presented by team member Joanna Sharman in April 2015 at the BPS Focused Meeting: Exploiting the new pharmacology and application to drug discovery in Edinburgh.
Reactome is a free, open-source, curated and peer-
reviewed knowledge-base of biomolecular pathways.
Its aim is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education.
Drug-to-protein mappings in the Guide to PHARMACOLOGY: Utility as a target va...Guide to PHARMACOLOGY
The Guide to Pharmacology database (GtoPdb) provides expertly curated information on drug-protein interactions and targets of approved and investigational drugs. It currently includes data on interactions between over 1400 protein targets and 7700 ligands derived from over 5000 literature references. The database covers major target classes and provides a useful resource for target validation and drug discovery. Future plans include regular updates with new target and drug data as well as potential specialty sub-portals within the database.
Sorting bioactive wheat from database chaff: Challenges of discerning correct...Guide to PHARMACOLOGY
Since 2009 the Guide to PHARMACOLOGY database (GtoPdb) team have curated 7586 ligands from papers, including approved drugs, clinical candidates , research compounds peptides and clinical antibodies (PMID 24234439). As PubChem pushes towards 70 million compound identifiers (CIDs), we have noticed the problem
of “multiplexing” during the curation of 5713 small molecules as CIDs. we encountered many representations (i.e. different CIDs) of the same pharmacological entities. Three types of variation dominate: stereochemistry, mixtures and isotopic analogues. These are known constitutive issues for chemical databases but in
recent years we observed this multiplexing was reaching
problematic proportions (i.e. more chaff), especially for clinically used drugs (i.e. proportionally less wheat)
Sorting bioactive wheat from database chaffChris Southan
Abstract
Databases of bioactive compounds are crucial for pharmacology, drug discovery and chemical genomics as public sources approach ~ 100 million records. However, in recent years this famine-to-feast presents difficulties for searching chemical structures and linked activity data, particularly for those unfamiliar with the constitutive challenges of molecular representation in silico (PMID 25415348). A key problem is entries of structural variants of “the same thing” as pharmacological entities (i.e. representational multiplexing). For example, a 2009 comparison of three database subsets of ~1200 approved drugs recorded only 807 structures in-common (PMID 20298516). In addition, published counts of approved drugs vary widely. These issues have been continually encountered by the Guide to PHARMACOLOGY database (GtoPdb) team that, since 2009, has achieved the curation of ~5500 small molecules (including approved drugs) from papers. Concomitantly, we have noticed an increase in multiplexing as PubChem pushes towards 65 million compound identifiers (CIDs). Since one of our key objectives is to affinity-map ligands to their targets, we decided to assess this multiplexing problem in order to optimise our curation rules. The results have implications for the entire bioactivity information space. We began by compiling CID sets for seven different sources within PubChem encompassing approved drugs. Initially a 7x7 pairwise comparison matrix indicated low overlap between these sources. A Venn diagram was then made from the approved drug CIDs mapped by DrugBank, Therapeutic Target Database and ChEMBL. At 749, the three-way intersect was less than 35% of the union of all CIDs covered by the sets. Strikingly, this looks worse that the 2009 study (although the sources and comparison methods were different). We will present further analyses that go some way towards explaining these results. One of these is determining “same connectivity” statistics inside PubChem as a measure of multiplexing. For DrugBank, each approved drug was related to, on average, 19 different CIDs as structural variants. Analysis of multiplexing confirmed trends we had observed during individual drug curation. This included ~ 30% stereoisomer enumerations but, surprisingly, ~70% isotopic derivatives, dominated by patent-derived virtual deuteration. We also established the ratio of submissions (SIDs) to CIDs was 78. The paradox was that, despite this high “majority vote” support for approved drug CIDs curated by DrugBank, only 55% were in the 3-way consensus (figures for the other two curated sources were similar). Analysing by year in PubChem indicated how the recent expansion of vendor and patent-extraction structures contributes to both multiplexing and the SID: CID ratio. While approved drugs are strongly impacted, associated problems, such as split activity data and deciding the “correct” structures, affect essentially all public drug discovery chem
The Protein Data Bank (PDB) is the single worldwide database that stores the 3D structural data of large biological molecules such as proteins and nucleic acids. It contains data submitted by researchers from around the world. The PDB is operated by three member organizations and uses standardized file formats like PDB, mmCIF, and PDBML to store and represent structural data. Secondary databases categorize the PDB data in different ways, such as by structure, function, or evolutionary relationships. Visualization programs can be used to view PDB file contents. PDBWiki allows collaborative discussion and annotation of PDB structures, complementing the PDB's role as a primary data archive.
This document discusses the extraction of key relationships (D-A-R-C-P) reported in biomedical literature where a bioactivity (A) and result (R) are reported for a chemical structure (C) that modulates a protein target (P). It analyzes the statistics of DARCP entity accumulation from three manually curated databases and compares it to PubChem. While public databases have captured around 18% of known human protein targets, commercial databases have captured around 4 times more DARCP relationships through greater curation resources. The future of DARCP extraction depends on increased natural language processing, open access policies, and databases facilitating the input of these relationships.
The Prototype of Standalone Diagnostic Report Editor as a Proof-of-Concept for an Interoperable Implementation of Health Level Seven Clinical Document Architecture Standard (HL7 CDA) not Integrated with Electronic Health Record (EHR) System
The document provides information on regulatory submissions in Japan. It discusses:
- Japan's pharmaceutical market size and aging population trends.
- The Ministry of Health and Pharmaceutical and Medical Devices Agency (PMDA) oversee drug regulation. Applications are submitted to PMDA for approval.
- The Common Technical Document (CTD) format is used for submissions, which organizes information into five modules covering administrative data, summaries, quality, nonclinical studies, and clinical studies.
This document summarizes the goals and steps taken to scrape data from PDF files on the Banking Organization Systemic Risk Report website. It involved scraping the HTML, cleaning and formatting the raw data from the PDFs, and performing exploratory data analysis on the data in Tableau. Key steps included fetching the HTML using libraries in Python, extracting tables and text from PDFs using regular expressions, and creating visualizations of indicators like exposures, assets, liabilities, and scores in Tableau to analyze systemic risk across banks.
Exploiting PubChem for drug discovery based on natural productsSunghwan Kim
Presented at the 256th American Chemical Society (ACS) National Meeting in Boston, MA (August 19, 2018).
==== Abstract ====
PubChem is one of the largest sources of publicly available chemical information, with more than 242.3 million depositor-provided substance descriptions, 94.7 million unique chemical structures, and 234.8 million bioactivity outcomes from 1.25 million assays covering around ten thousand unique protein target sequences. This presentation provides an overview of PubChem’s data, tools, and services useful for drug discovery based on natural products.
PubChem contains a large amount of bioactivity data, most of which are generated from high-throughput screening (HTS). However, these data also include a substantial amount of bioactivity information extracted from scientific articles published in journals in the chemical biology, medicinal chemistry, and natural product domains, thanks to data contribution by other databases like ChEMBL, Guide to Pharmacology, BindingDB, and PDBbind. In addition, through data integration with other databases such as DrugBank, HSDB, and HMDB, PubChem contains a wide range of annotations useful for drug discovery, including pharmacology, toxicology, drug target, metabolism, chemical vendors, scientific articles, patents, and many others.
PubChem supports various types of chemical structure searches, including identify search, 2-D and 3-D similarity searches, substructure and superstructure searches, molecular formula search. It also provides multiple programmatic access routes, including E-Utilities, Power User Gateway (PUG), PUG-SOAP, PUG-REST, and PUG-View, allowing one to build an automated workflow that takes advantage of information contained in PubChem. In addition, through PubChemRDF, users can integrate PubChem’s data into their own in-house data on a local computing machine.
Similar to Poster PubMed-to-PubChem connectivity between GtoPdb and BJP (20)
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an expert-driven, open database of pharmacological targets and the substances that act on them. It contains information on over 1,800 drug targets and 1,100 related proteins. The database is curated by 500 experts and provides detailed pharmacological data as well as overviews of key properties and ligands. Specialized extensions of GtoPdb include guides to immunopharmacology and malaria pharmacology that connect their fields to drug discovery. The database is continuously updated with new targets, ligands, features and access methods.
Presentation by Dr. Elena Faccenda on the IUPHAR/BPS Guide to Immunopharmacology at the 39° Congresso Nazionale della Società Italiana di Farmacologia in Florence, Nov 2019
This document discusses the IUPHAR/BPS Guide to Pharmacology database and related resources. It provides open access information on pharmacological targets and the substances that act on them. It includes over 1,700 human drug targets, 9,700 ligands including 1,300 approved drugs. Related databases include the Guide to Immunopharmacology and Guide to Malaria Pharmacology. The databases are regularly updated and include links to other resources to enable interoperability.
1) Researchers have created a new online resource called the IUPHAR/MMV Guide to Malaria Pharmacology (GtoMPdb) to curate information on antimalarial compounds and their molecular targets in Plasmodium.
2) The database currently contains 25 Plasmodium molecular targets and 57 antimalarial ligands that were manually curated from scientific literature.
3) A new customized online portal provides open access to the antimalarial data and allows browsing by parasite lifecycle stage, target species, and other features to help malaria research.
Dr. Simon D. Harding of the University of Edinburgh created a knowledge-base that connects immunology and pharmacology. The knowledge-base links immunological targets and ligands to cell types and diseases. It is part of the IUPHAR/BPS Guide to Pharmacology, an open database of drug targets and ligands including approved drugs. A new search tool allows searching of pharmacological information. Dr. Harding also aims to curate data on antimalarial compounds and their molecular targets in Plasmodium through the IUPHAR/MMV Guide to Malaria Pharmacology.
Poster on GtoImmuPdb presented at European Congress of Immunology (Amsterdam, Sep 2018). Overview of the main data types and features included in this extension to the IUPHAR/BPS Guide to PHARMACOLOGY
The document provides a status report on the Guide to Immunopharmacology database (GtoImmuPdb). It discusses developments including the addition of disease data, graphical browsing of cell type data, and process data. The database is in beta version 3 and undergoing user testing. Over 500 targets and 1,000 ligands have been curated from the literature. On the curation side, efforts are focused on expanding the literature collection and annotating new targets and ligands. The database is preparing for its official launch in October 2018.
The IUPHAR/BPS Guide to PHARAMCOLOGY in 2018: new features and updatesGuide to PHARMACOLOGY
2018 update poster for the IUPHAR/BPS Guide to PHARMACOLOGY. Giving details of new features and updates. To be presented at Pharmacology Futures, Edinburgh, May 2018; ELIXIR-All Hands, Berlin, June 2018 and World Congress of Pharmacology, Kyoto, Japan, July 2018
Updated poster following beta v3 release. In preparation for Pharmacology Futures, Edinburgh Immunology Symposium and Word Congress of Pharmacology (Kyoto)
IUPHAR/BPS Guide to PHARMACOLOGY in 2017: new features and updatesGuide to PHARMACOLOGY
This document summarizes updates to the IUPHAR/BPS Guide to PHARMACOLOGY database. It provides expert curated data on human drug targets and ligands. Recent additions include new target families, ligands, and links to immunopharmacology data. New features include download options, search tools, and organization of ligand families. The database is maintained by an international team and network of scientists and provides a resource for pharmacology education and research.
These slides will be presented at the Pharmacology 2017 meeting in London during the following session:
Abstract Number: OB073
Abstract Title: Capturing new BIA 10-2474 molecular data in the IUPHAR/BPS Guide to PHARMACOLOGY
Date: Wednesday, December 13, 2017, 11:30 AM
Oral Session: Oral Communications: Mixed Tracks
This comprehensive slide deck is provided for use by those who are teaching and presenting on the IUPHAR/BPS Guide to PHARMACOLOGY. Includes:
- Overview of NC-IUPHAR
- Background to GtoPdb
- Screenshots of the website and search tools
- Recent content expansions
- Other features and initiatives including the Guide to IMMUNOPHARMACOLOGY
This slide set updates the previous set from 2014/15 available at https://www.slideshare.net/GuidetoPHARM/iupharbps-guide-to-pharmacology-generic-slideset
A general poster about the IUPHAR/BPS Guide to PHARMACOLOGY, updated for 2017. This works well used as a handout or pinned on departmental noticeboards.
IUPHAR Guide to IMMUNOPHARMACOLOGY poster. Presented at the BSI Congress 2017, Brighton, UK (6th December 2017) and at Pharmacology 2017, London, UK (13th December 2017.
This document describes updates to the Guide to PHARMACOLOGY (GtoPdb) database in 2017, including new features such as:
1) Organization of drug targets into families and subclasses for easier browsing, and organization of ligands into related families and groups.
2) Ability to visualize ligand binding affinities across species through activity graphs.
3) SynPHARM database for finding ligand binding sequences that can be engineered into synthetic proteins.
4) Expanded content with over 1,700 drug targets, 9,000 ligands, and options to search or download data in various formats.
Microbial interaction
Microorganisms interacts with each other and can be physically associated with another organisms in a variety of ways.
One organism can be located on the surface of another organism as an ectobiont or located within another organism as endobiont.
Microbial interaction may be positive such as mutualism, proto-cooperation, commensalism or may be negative such as parasitism, predation or competition
Types of microbial interaction
Positive interaction: mutualism, proto-cooperation, commensalism
Negative interaction: Ammensalism (antagonism), parasitism, predation, competition
I. Mutualism:
It is defined as the relationship in which each organism in interaction gets benefits from association. It is an obligatory relationship in which mutualist and host are metabolically dependent on each other.
Mutualistic relationship is very specific where one member of association cannot be replaced by another species.
Mutualism require close physical contact between interacting organisms.
Relationship of mutualism allows organisms to exist in habitat that could not occupied by either species alone.
Mutualistic relationship between organisms allows them to act as a single organism.
Examples of mutualism:
i. Lichens:
Lichens are excellent example of mutualism.
They are the association of specific fungi and certain genus of algae. In lichen, fungal partner is called mycobiont and algal partner is called
II. Syntrophism:
It is an association in which the growth of one organism either depends on or improved by the substrate provided by another organism.
In syntrophism both organism in association gets benefits.
Compound A
Utilized by population 1
Compound B
Utilized by population 2
Compound C
utilized by both Population 1+2
Products
In this theoretical example of syntrophism, population 1 is able to utilize and metabolize compound A, forming compound B but cannot metabolize beyond compound B without co-operation of population 2. Population 2is unable to utilize compound A but it can metabolize compound B forming compound C. Then both population 1 and 2 are able to carry out metabolic reaction which leads to formation of end product that neither population could produce alone.
Examples of syntrophism:
i. Methanogenic ecosystem in sludge digester
Methane produced by methanogenic bacteria depends upon interspecies hydrogen transfer by other fermentative bacteria.
Anaerobic fermentative bacteria generate CO2 and H2 utilizing carbohydrates which is then utilized by methanogenic bacteria (Methanobacter) to produce methane.
ii. Lactobacillus arobinosus and Enterococcus faecalis:
In the minimal media, Lactobacillus arobinosus and Enterococcus faecalis are able to grow together but not alone.
The synergistic relationship between E. faecalis and L. arobinosus occurs in which E. faecalis require folic acid
Mechanics:- Simple and Compound PendulumPravinHudge1
a compound pendulum is a physical system with a more complex structure than a simple pendulum, incorporating its mass distribution and dimensions into its oscillatory motion around a fixed axis. Understanding its dynamics involves principles of rotational mechanics and the interplay between gravitational potential energy and kinetic energy. Compound pendulums are used in various scientific and engineering applications, such as seismology for measuring earthquakes, in clocks to maintain accurate timekeeping, and in mechanical systems to study oscillatory motion dynamics.
BIRDS DIVERSITY OF SOOTEA BISWANATH ASSAM.ppt.pptxgoluk9330
Ahota Beel, nestled in Sootea Biswanath Assam , is celebrated for its extraordinary diversity of bird species. This wetland sanctuary supports a myriad of avian residents and migrants alike. Visitors can admire the elegant flights of migratory species such as the Northern Pintail and Eurasian Wigeon, alongside resident birds including the Asian Openbill and Pheasant-tailed Jacana. With its tranquil scenery and varied habitats, Ahota Beel offers a perfect haven for birdwatchers to appreciate and study the vibrant birdlife that thrives in this natural refuge.
Discovery of Merging Twin Quasars at z=6.05Sérgio Sacani
We report the discovery of two quasars at a redshift of z = 6.05 in the process of merging. They were
serendipitously discovered from the deep multiband imaging data collected by the Hyper Suprime-Cam (HSC)
Subaru Strategic Program survey. The quasars, HSC J121503.42−014858.7 (C1) and HSC J121503.55−014859.3
(C2), both have luminous (>1043 erg s−1
) Lyα emission with a clear broad component (full width at half
maximum >1000 km s−1
). The rest-frame ultraviolet (UV) absolute magnitudes are M1450 = − 23.106 ± 0.017
(C1) and −22.662 ± 0.024 (C2). Our crude estimates of the black hole masses provide log 8.1 0. ( ) M M BH = 3
in both sources. The two quasars are separated by 12 kpc in projected proper distance, bridged by a structure in the
rest-UV light suggesting that they are undergoing a merger. This pair is one of the most distant merging quasars
reported to date, providing crucial insight into galaxy and black hole build-up in the hierarchical structure
formation scenario. A companion paper will present the gas and dust properties captured by Atacama Large
Millimeter/submillimeter Array observations, which provide additional evidence for and detailed measurements of
the merger, and also demonstrate that the two sources are not gravitationally lensed images of a single quasar.
Unified Astronomy Thesaurus concepts: Double quasars (406); Quasars (1319); Reionization (1383); High-redshift
galaxies (734); Active galactic nuclei (16); Galaxy mergers (608); Supermassive black holes (1663)
Compositions of iron-meteorite parent bodies constrainthe structure of the pr...Sérgio Sacani
Magmatic iron-meteorite parent bodies are the earliest planetesimals in the Solar System,and they preserve information about conditions and planet-forming processes in thesolar nebula. In this study, we include comprehensive elemental compositions andfractional-crystallization modeling for iron meteorites from the cores of five differenti-ated asteroids from the inner Solar System. Together with previous results of metalliccores from the outer Solar System, we conclude that asteroidal cores from the outerSolar System have smaller sizes, elevated siderophile-element abundances, and simplercrystallization processes than those from the inner Solar System. These differences arerelated to the formation locations of the parent asteroids because the solar protoplane-tary disk varied in redox conditions, elemental distributions, and dynamics at differentheliocentric distances. Using highly siderophile-element data from iron meteorites, wereconstruct the distribution of calcium-aluminum-rich inclusions (CAIs) across theprotoplanetary disk within the first million years of Solar-System history. CAIs, the firstsolids to condense in the Solar System, formed close to the Sun. They were, however,concentrated within the outer disk and depleted within the inner disk. Future modelsof the structure and evolution of the protoplanetary disk should account for this dis-tribution pattern of CAIs.
Order : Trombidiformes (Acarina) Class : Arachnida
Mites normally feed on the undersurface of the leaves but the symptoms are more easily seen on the uppersurface.
Tetranychids produce blotching (Spots) on the leaf-surface.
Tarsonemids and Eriophyids produce distortion (twist), puckering (Folds) or stunting (Short) of leaves.
Eriophyids produce distinct galls or blisters (fluid-filled sac in the outer layer)
The Limited Role of the Streaming Instability during Moon and Exomoon FormationSérgio Sacani
It is generally accepted that the Moon accreted from the disk formed by an impact between the proto-Earth and
impactor, but its details are highly debated. Some models suggest that a Mars-sized impactor formed a silicate
melt-rich (vapor-poor) disk around Earth, whereas other models suggest that a highly energetic impact produced a
silicate vapor-rich disk. Such a vapor-rich disk, however, may not be suitable for the Moon formation, because
moonlets, building blocks of the Moon, of 100 m–100 km in radius may experience strong gas drag and fall onto
Earth on a short timescale, failing to grow further. This problem may be avoided if large moonlets (?100 km)
form very quickly by streaming instability, which is a process to concentrate particles enough to cause gravitational
collapse and rapid formation of planetesimals or moonlets. Here, we investigate the effect of the streaming
instability in the Moon-forming disk for the first time and find that this instability can quickly form ∼100 km-sized
moonlets. However, these moonlets are not large enough to avoid strong drag, and they still fall onto Earth quickly.
This suggests that the vapor-rich disks may not form the large Moon, and therefore the models that produce vaporpoor disks are supported. This result is applicable to general impact-induced moon-forming disks, supporting the
previous suggestion that small planets (<1.6 R⊕) are good candidates to host large moons because their impactinduced disks would likely be vapor-poor. We find a limited role of streaming instability in satellite formation in an
impact-induced disk, whereas it plays a key role during planet formation.
Unified Astronomy Thesaurus concepts: Earth-moon system (436)
Candidate young stellar objects in the S-cluster: Kinematic analysis of a sub...Sérgio Sacani
Context. The observation of several L-band emission sources in the S cluster has led to a rich discussion of their nature. However, a definitive answer to the classification of the dusty objects requires an explanation for the detection of compact Doppler-shifted Brγ emission. The ionized hydrogen in combination with the observation of mid-infrared L-band continuum emission suggests that most of these sources are embedded in a dusty envelope. These embedded sources are part of the S-cluster, and their relationship to the S-stars is still under debate. To date, the question of the origin of these two populations has been vague, although all explanations favor migration processes for the individual cluster members. Aims. This work revisits the S-cluster and its dusty members orbiting the supermassive black hole SgrA* on bound Keplerian orbits from a kinematic perspective. The aim is to explore the Keplerian parameters for patterns that might imply a nonrandom distribution of the sample. Additionally, various analytical aspects are considered to address the nature of the dusty sources. Methods. Based on the photometric analysis, we estimated the individual H−K and K−L colors for the source sample and compared the results to known cluster members. The classification revealed a noticeable contrast between the S-stars and the dusty sources. To fit the flux-density distribution, we utilized the radiative transfer code HYPERION and implemented a young stellar object Class I model. We obtained the position angle from the Keplerian fit results; additionally, we analyzed the distribution of the inclinations and the longitudes of the ascending node. Results. The colors of the dusty sources suggest a stellar nature consistent with the spectral energy distribution in the near and midinfrared domains. Furthermore, the evaporation timescales of dusty and gaseous clumps in the vicinity of SgrA* are much shorter ( 2yr) than the epochs covered by the observations (≈15yr). In addition to the strong evidence for the stellar classification of the D-sources, we also find a clear disk-like pattern following the arrangements of S-stars proposed in the literature. Furthermore, we find a global intrinsic inclination for all dusty sources of 60 ± 20◦, implying a common formation process. Conclusions. The pattern of the dusty sources manifested in the distribution of the position angles, inclinations, and longitudes of the ascending node strongly suggests two different scenarios: the main-sequence stars and the dusty stellar S-cluster sources share a common formation history or migrated with a similar formation channel in the vicinity of SgrA*. Alternatively, the gravitational influence of SgrA* in combination with a massive perturber, such as a putative intermediate mass black hole in the IRS 13 cluster, forces the dusty objects and S-stars to follow a particular orbital arrangement. Key words. stars: black holes– stars: formation– Galaxy: center– galaxies: star formation
Hariyalikart Case Study of helping farmers in Biharrajsaurav589
Helping farmers all across India through our latest technologies of modern farming like drones for irrigation and best pest control For more visit : https://www.hariyalikart.com/case-study
Rodents, Birds and locust_Pests of crops.pdfPirithiRaju
Mole rat or Lesser bandicoot rat, Bandicotabengalensis
•Head -round and broad muzzle
•Tail -shorter than head, body
•Prefers damp areas
•Burrows with scooped soil before entrance
•Potential rat, one pair can produce more than 800 offspringsin one year
Signatures of wave erosion in Titan’s coastsSérgio Sacani
The shorelines of Titan’s hydrocarbon seas trace flooded erosional landforms such as river valleys; however, it isunclear whether coastal erosion has subsequently altered these shorelines. Spacecraft observations and theo-retical models suggest that wind may cause waves to form on Titan’s seas, potentially driving coastal erosion,but the observational evidence of waves is indirect, and the processes affecting shoreline evolution on Titanremain unknown. No widely accepted framework exists for using shoreline morphology to quantitatively dis-cern coastal erosion mechanisms, even on Earth, where the dominant mechanisms are known. We combinelandscape evolution models with measurements of shoreline shape on Earth to characterize how differentcoastal erosion mechanisms affect shoreline morphology. Applying this framework to Titan, we find that theshorelines of Titan’s seas are most consistent with flooded landscapes that subsequently have been eroded bywaves, rather than a uniform erosional process or no coastal erosion, particularly if wave growth saturates atfetch lengths of tens of kilometers.
Mapping the Growth of Supermassive Black Holes as a Function of Galaxy Stella...Sérgio Sacani
The growth of supermassive black holes is strongly linked to their galaxies. It has been shown that the population
mean black hole accretion rate (BHAR) primarily correlates with the galaxy stellar mass (Må) and redshift for the
general galaxy population. This work aims to provide the best measurements of BHAR as a function of Må and
redshift over ranges of 109.5 < Må < 1012 Me and z < 4. We compile an unprecedentedly large sample with 8000
active galactic nuclei (AGNs) and 1.3 million normal galaxies from nine high-quality survey fields following a
wedding cake design. We further develop a semiparametric Bayesian method that can reasonably estimate BHAR
and the corresponding uncertainties, even for sparsely populated regions in the parameter space. BHAR is
constrained by X-ray surveys sampling the AGN accretion power and UV-to-infrared multiwavelength surveys
sampling the galaxy population. Our results can independently predict the X-ray luminosity function (XLF) from
the galaxy stellar mass function (SMF), and the prediction is consistent with the observed XLF. We also try adding
external constraints from the observed SMF and XLF. We further measure BHAR for star-forming and quiescent
galaxies and show that star-forming BHAR is generally larger than or at least comparable to the quiescent BHAR.
Unified Astronomy Thesaurus concepts: Supermassive black holes (1663); X-ray active galactic nuclei (2035);
Galaxies (573)
Poster PubMed-to-PubChem connectivity between GtoPdb and BJP
1. 3. PubChem < > PubMed < > BJP
2. GtoPdb ligand -to-journal mappings
6. References
Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK.
www.guidetopharmacology.org enquiries@guidetopharmacology.org @GuidetoPHARM
Navigating links between structures and papers:
PubMed-to-PubChem connectivity between the IUPHAR/BPS
Guide to PHARMACOLOGY and British Journal of Pharmacology
Supported by:
We especially thank all contributors, collaborators and NC-IUPHAR members
1. Introduction
The pharmacological literature connects activity data reported for drugs and
research compounds to their explicit chemical structures. However, the traditional
entombing of these relationships for millions of compounds among millions of PDFs
is retrospectively acknowledged as massively problematic. The situation is
ameliorated by a range of resources that extract the entity and data relationships the
authors put “in” to the PDFs back “out” into structured database records. The
IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) has been doing this for over a
decade by expert curation of structures, activity data and targets [1]. Our cross-
reference total has reached 30,000 with an approximately equal split between
citations related to targets or associated with ligand interactions [2]. As a
collaboration, we have been submitting ligand related citations to PubChem (PC)
who then link these into PubMed (PM). This means pharmacologists can navigate
from our GtoPdb ligand entries “out” via the PubMed Identifier (PMID) and either the
PC Substance Identifiers (SIDs that are unique to us as a submitter) or Compound
Identifiers (CIDs that merge all submitters). This work outlines our linking process in
general and for the British Journal of Pharmacology (BJP) in particular.
There are multiple sources and different contexts of PC < > PM links [3]. Data
contributors provide chemical information extracted from the scientific literature through
manual curation or data mining. Table 1 summarises the top-4 contributors by the count
of depositor-provided cross-references between PC SIDs and PMIDs.
Table 1 (adapted from [3])
While GtoPdb ranks 3rd for the manually curated contributors we have the highest
stringency of target-ligand-PMID links. Note that the 14.3 K encompasses all the papers
represented by our complete Figure 1 list. Our own analysis drilled down to selected
individual journals. The results generated for BJP are shown below.
Table 2
The interpretation of all rows in Table 2 cannot be expanded here. However, the
GtoPdb SID counts (blue) establish we are the main contributor of BJP links in recent
years and for key compounds (i.e. what those publications are “about”) back to 2010.
We extract approximately 10% of BJP papers by our criteria for database records.
Figure 1. Examples of various kinase database tables
1. Harding SD, et al. (2018) The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: Updates and expansion to encompass
the new Guide to IMMUNOPHARMACOLOGY. Nucl. Acids Res. 46 (Database Issue). doi: 10.1093/nar/gkx1121.
2. https://blog.guidetopharmacology.org/2017/10/18/gtopdb-nar-database-issue-2018-journal-to-database-connectivity-and-
journal-to-gtopdb-links/
3. Kim S. et al. (2016) Literature information in PubChem: associations between PubChem records and scientific articles. J
Cheminformatics. 8:32. doi: 10.1186/s13321-016-0142-6
4. McGrath JC et al (2015) BJP is linking articles to the IUPHAR/BPS Guide to PHARMACOLOGY. BJP, 172(12):2929-32.
GtoPdb is an ELIXIR UK node resource
4. Virtuous circle: BJP < > GtoPdb < >PubChem < > PubMed
This section illustrates how linkage navigation can be followed from our entry for
PXS4728A. This is retrievable from the GtoPdb search box as ligand 9346. Our
PubChem entry is SID 328083448 and the BJP paper is PMID: 27495192. The series
of connections that users can simply click on are shown below in Figure 2.
The navigation in Fig.2. can be explained as a series of steps;
1. From the GtoPdb ligand entry (A) clicking the “Reference” goes to across to PM and
the BJP abstract (B).
2. The abstract facet (C) shows “Related Information” that includes links to PC SIDs
and CIDs.
3. Clicking on the Substance link takes users to our SID entry. Going down to
“Depositor Comments” (D) displays the same information we curated into the
summary part of the GtoPdb ligand entry.
4. The “Depositor Supplied PubMed Citations” section of the SID (E) indicates the two
references. In this case J. Med. Chem. is our primary reference and the BJP paper a
secondary reference.
5. These links are reciprocal so users can navigate into the circle via any of them.
Christopher Southan, Elena Faccenda, Joanna L. Sharman, Simon D. Harding, Adam J. Pawson, Jamie A. Davies
5. Conclusions
• Traversing publications and bioactive chemistry databases is becoming a core
competence for pharmacologists and should thus be part of their education.
• For PC as the major source of links, understanding the different types is daunting.
• However, we show in Fig 2 that, starting from GtoPdb as an easy to use entry
point, users can simply click-navigate between PM and PC in an informative
virtuous circle
• For the example shown, both BJP and the article authors will benefit from user traffic
through these links
• As featured in [3] GtoPdb is a major contributor of curated links to key bioactive
structures inside PC not just for the BJP but all journals curated by us
• However, Table 2 shows PC connections for BJP papers are complex
• We have identified specificity issues for non-GtoPdb chemistry linking sources in PC
including for the automated extraction of abstracts via IBM patent processing
• Note our curated GtoPdb > BJP linking is complemented by the BJP > GtoPdb out-
links added since 2015 and recently converted to in-line links [4]
The PMIDs we link to ligands are
predominantly what we term
primary references, selected for
curation because they include
the quantitative in vitro activity
against target proteins along with
the specification of ligand
structures, generally related to
drug R&D. We also capture what
we term secondary papers that
specify in vivo activities (e.g.
rodent data) and in fewer cases
also tertiary references as clinical
reports. Figure 1 shows the
journal distribution of ligand
associated references. While J
Med. Chem. tops the primary
citations BJP is 6th with a mixture
of primary and secondary
papers.
´
Figure 1. Top-20 Journals for ligand citations
Figure 2. The arrows and highlighted
sections indicate inter-database links
(A)
(B)
(C)
(D)
(E)