ELIXIR Database Provider Survey
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The survey characterized 73 biomolecular databases to understand their funding, usage, and sustainability. It found that 66% had funding for one year or less, with only 6.5% funded for over five years. Usage was highest for databases with unique users, with the most used database receiving over 60 million hits per month. The results will help the ELIXIR infrastructure plan support for biomolecular databases and ensure long-term access to biological data.
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![Introduction The mission of the European Life sciences Infrastructure for Biological Information (ELIXIR) is to enable a sustainable infrastructure for biological information to support life science research. For the information gathering phase a survey of biomolecular resources has been carried out. After a pilot survey of 50 databases a final list of 73 questions was optimised to provide detailed information about locations, data types, funding, usage metrics, citations and other statistics relevant to database operation. We prepared mailing lists using the Nucleic Acids Research Molecular Biology Database Collection from Jan 2008 and by running PubMed queries for updates during 2008/2009. The proportion of published databases that included ELIXIR-affiliated countries was 38%. EUROPEAN LIFE SCIENCE INFRASTRUCTURE FOR BIOLOGICAL INFORMATION (ELIXIR) The ELIXIR Database Provider Survey Chris Southan, Andrew Lyall and Graham Cameron EMBL-EBI Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Results Status and Distribution: From 531 database providers circulated between Oct08 and Apr09 inspection of the URLs showed 63 that were either not live or not updated since 2005. The update status was unclear for a further 78. We received 208 completed survey returns the geographical distribution of which is show in fig.1 Fig.1 Survey Returns by Country Table 1. Funding Sustainability, expressed as a % of 201 responses Funding Sustainability: When asked about funding duration the answers (Table 1) showed that 66% of respondents had one year or less and that only 6.5% had funding of five years or more. Costs: The distribution of reported costs (Fig.2) shows that ~ 25 databases account for ~ 90% of a total investment to date of €308 million with annual costs of €35 million. However ~ 1/3 of responders report no costs, speculatively because these were predominantly smaller databases sustained indirectly by research project funds. Fig.2 Costs per database in €K Conclusions The results of this survey will be invaluable for planning the ELIXIR Data Resources strategy. Only a selection of the data could be presented here and additional documentation is in progress. Further information is available at www.elixir-europe.org, including listings of questions, the databases, a map display and slides from the Data Resources Work Package 2 presented at the May 2009 Stakeholders meeting. On behalf of all ELIXIR Stakeholders we would like to express our thanks to those who took the time and effort to complete the questionnaire. We would also draw you attention to an accompanying poster on the ELIXIR Database User Survey by S. Palcy and A. de Daruvar. ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Usage Metrics: Considered as a reflection of real-world usage the order of preference was unique users (shown below in fig.3) followed by hits and sessions. Cumulative hits per-month was 60 million for 200 respondents. Fig.4 Institutional Distribution Fig.3 Counts of Unique Users-per month (rightmost is UniProt) Databases per-institution: Approximately 100 separate institutions were covered by the returns. The distribution is shown in fig.4. The majority of institutions had only one responding database. Not assured 36% Assured for at least 1 year 30% Assured for at least 3 years 27% Assured for at least 5 years 3.0% Assured for more than 5 years 3.5% We are considering commercialisation 0.5%](https://image.slidesharecdn.com/elixirposter-12442117786-phpapp01/85/ELIXIR-Database-Provider-Survey-1-320.jpg)
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http://scribd.com/doc/239851110Philipp Aerni — Lock in situations in the global debates on climate change an...
Philipp Aerni — Lock in situations in the global debates on climate change an...Climate Change @ The International Food Policy Research Institute
The Chinese Academy of Agricultural Sciences (CAAS) and the International Food Policy Research Institute (IFPRI) jointly hosted the International Conference on Climate Change and Food Security (ICCCFS) November 6-8, 2011 in Beijing, China. This conference provided a forum for leading international scientists and young researchers to present their latest research findings, exchange their research ideas, and share their experiences in the field of climate change and food security. The event included technical sessions, poster sessions, and social events. The conference results and recommendations were presented at the global climate talks in Durban, South Africa during an official side event on December 1.NISO Working Group Connection Live! Research Data Metrics Landscape: An Updat...
NISO Working Group Connection Live! Research Data Metrics Landscape: An Updat...National Information Standards Organization (NISO)
This document summarizes a presentation on research data metrics from the NISO Altmetrics Working Group B. It discusses various metrics for research data, including citations of datasets and metadata, full-text search of datasets, downloads, and usage statistics. It also describes projects from DataCite and the Making Data Count initiative that are working to develop standard metrics for research data and make them available via APIs. Future work discussed includes analyzing networks of linked datasets and second-order citations.STI 2014 Schomaker & Noyons - methodological study to structure liquid biofue...
sti2014 presentation title
A methodological study to structure liquid biofuel science and put its publication dynamics into perspective
sti2014 paper abstract
Climate change is unequivocal, human influence on the process is clear, and substantial and sustained reductions of greenhouse gas emissions will be required to mitigate and adapt to it. An early global response has been to use liquid biofuel for transport, a development that has triggered a vivid public debate. We try to provide insight in interactions, and the timing thereof, in this debate between science, policy and society. We look at the entire biofuel knowledge base, which is a heterogeneous body of scientific publications and applied ‘grey’ literature. As a first step we present this paper on the methodology applied to structure the scientific part of biofuel knowledge and to put its time dynamics in perspective. We combine quantitative bibliometric data and contextual, qualitative expert interpretation. We used the Web of Science and the CWTS global science classification system to create a body of publications, structured into biofuel related clusters that are based on citation relations and patterns. Each cluster contains both ‘pure’ liquid biofuel publications and surrounding articles that are relevant but not specific enough to be part of the biofuels core. We annotated the selected clusters, extracted data on key players, calculated cluster ages, and presented the number of publications per year for each cluster graphically, always distinguishing between core biofuel- and related surrounding articles. In our analysis, and the main reason for this paper, we then illustrate that it is the actual integration of these different types of detailed data that provides additional information to arrive at an understanding of publication dynamics.
Biobanks: Patients’ Role and Expectations
Fabrizia BIGNAMI, PhD
Eurordis Therapeutic Development Director. EuroBioBank Administrative Coordinator. www.eurordis.org
www.eurobiobank.org
NRNB Annual Report 2012
This document provides an annual progress report for the National Resource for Network Biology (NRNB) for the period of May 1, 2011 to April 30, 2012. It summarizes the following:
1) Advances made in developing algorithms to identify network modules and use modules as biomarkers for disease. This includes methods to capture complex logical relationships within modules.
2) Progress on tools to enable new network analysis and visualization capabilities, including a new version of Cytoscape.
3) Growth of collaborations through the NRNB, which have nearly doubled over the past year to around 100 projects.
4) Continued development of the Cytoscape App Store to support the user and developer community.
SIF Presentation_Final
This document summarizes a research project on supervised injection facilities. It examines how such facilities can reduce overdose deaths, increase service provision, and decrease neighborhood crime reports based on evidence from 27 academic papers. The methodology includes a literature review to identify relationships between these variables and develop a causal loop diagram. Key findings are that supervised injection facilities can eliminate overdose deaths by allowing staff interventions and increase supportive service referrals. They may also reduce public injection and discarded needles while not increasing drug dealing in the vicinity. Limitations include the small paper sample and inconsistencies between facility outcomes.
Open Source Pharma: Game changing for innovative medicine
The document discusses the European Lead Factory project, which aims to establish an open source pharma industry for developing drugs for neglected diseases. It outlines the collaborative drug discovery process, including crowdsourcing chemical compounds and biological targets, screening compounds through a shared library, and making qualified hit lists available to partners. The goal is to generate value from publicly funded initiatives through this large-scale open innovation experiment.
Technopolis
This document summarizes the preliminary results of a stakeholder forum evaluating the Biobanking and BioMolecular resources Research Infrastructure (BBMRI). It analyzes 10 case studies of existing biobanks and finds that most are 5-7 years old and organized nationally. While collections vary greatly in size, there is a trend toward larger international networks. Funding models are mixed but indicate biobanking requires long-term investment and networking can reduce costs. A social network analysis found the core BBMRI members had a central role in previous EU projects, and more institutions should be included to expand the network.
Pathology is being disrupted by Data Integration, AI & Blockchain
This is an invited talk I gave at the 1st European Society for Pathology Academy in Waterloo (Belgium) in June 2018
Report on current m-library activity
The survey received 188 responses about current and planned mobile library initiatives. Many respondents' libraries are currently involved in initiatives (63%) such as mobile catalogues, websites, QR codes, and supporting mobile access to databases. Common mobile catalogue platforms included vendor modules, LibraryAnywhere, and WorldCat. Mobile websites were often developed in-house. QR codes were used for promotions, guides, and activities. Some libraries highlighted mobile-friendly resources on their website or created library apps. Others contributed mobile features to institutional apps. Looking ahead, many libraries plan further developments or are evaluating opportunities that mobile technologies offer users.
Research Policy Monitoring in the Era of Open Science & Big Data Workshop Report
Workshop on Research Policy Monitoring in the Era of Open Science and Big Data was a two day event, co-organised by OpenAIRE and Data4Impact, with support of Science Europe. The event explored mechanisms for research policy monitoring and indicators, and how to link these to infrastructure and services. The first day was focused on open science indicators as these emerge from national and EU initiatives, while the second day explored more advanced aspects of indicators for innovation and societal impact.
User-friendly bioinformatics (Monthly Informational workshop)
Pine Biotech conducts monthly informational workshops on the topics related to high-throughput data analysis, interpretation and integration. The workshops highlight our research tools and educational resources developed with collaborators in the US and across the world.
Annotation And Curation Of Human Genomic Variations An ELIXIR Implementation...
This document summarizes the results of an international survey conducted by ELIXIR, an intergovernmental organization that hosts life science resources. The survey aimed to understand how researchers use databases and tools for annotating and curating human genomic variations. It found that over 90 respondents from 18 countries considered several ELIXIR-supported resources as crucial or very important. Respondents acknowledged features promoted by ELIXIR like quality and maintenance of resources. The survey helps ELIXIR identify how to improve its resources and services for genomic research.
Eero Vuorio
The document summarizes the European Research Infrastructure for Biobanking and Biomolecular Resources (BBMRI) preparatory phase project. It discusses how biobanks across Europe have historically been small and fragmented. The BBMRI aims to integrate these resources to enable large-scale biomedical research. Over 50 institutions from 28 countries are involved in developing common standards, data sharing agreements, and a sustainable funding model to maximize the research potential of Europe's biological samples and data.
Georges Dagher
The document summarizes the European Research Infrastructure for Biobanking and Biomolecular Resources (BBMRI) preparatory phase project. It discusses how biobanks across Europe have historically been small and heterogeneous, hindering modern genetic research. The BBMRI aims to integrate existing biobanks and resources to create a large pan-European infrastructure following common standards. The preparatory phase involved over 50 institutions from 28 countries to assess resources and technologies and develop plans for a sustainable infrastructure to support research.
Eero Vuorio
The document summarizes the European Research Infrastructure for Biobanking and Biomolecular Resources (BBMRI) preparatory phase project. It discusses how biobanks across Europe have historically been small and fragmented. The BBMRI aims to integrate these resources to enable large-scale biomedical research by establishing common standards and open access. Over 50 institutions from 28 countries are involved in the preparatory phase to develop a prototype pan-European research infrastructure network for biobanking and biomolecular resources.
Workshop report
This document summarizes a workshop on methodology and indicators for assessing research and innovation held by the Data4Impact project. The project uses big data techniques to track the impacts of publicly-funded health research. In the morning, the project presented its analytical model and indicators for tracking outputs, academic impacts, economic impacts, and societal/health impacts. Discussion groups provided feedback on the indicators. In the afternoon, a panel of policymakers and funders discussed the relevance of the indicators and opportunities to improve the methodology. The workshop concluded by inviting participants to a future workshop on applying big data in scientometrics.
WP-2013-03-KOLMAT-GL-L
The document summarizes a case study comparing the results of using desk research and peer nomination to identify key opinion leaders (KOLs) in the indication of metastatic castrate-resistant prostate cancer (mCRPC) in Europe. Both methods yielded consistent top KOLs but also identified different KOLs, highlighting their complementary nature. Combining the methods provides a more comprehensive picture of the KOL landscape through a "Hybrid KOL Matrix" that segments KOLs by reputation and perception. This approach helps pharmaceutical companies design effective KOL engagement strategies tailored to different stages of the drug lifecycle and business needs.
Data4Impact booklet overview of results
Data4Impact booklet demonstrates linkages between data collected across the three dimensions of impact, including academic, economic and societal impact
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Social and Therapeutic Horticulture: The State of Practice in the United Kingdom
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Philipp Aerni — Lock in situations in the global debates on climate change an...
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Annotation And Curation Of Human Genomic Variations An ELIXIR Implementation...
More from Chris Southan
FAIR connectivity for DARCP
This document discusses challenges for making documents, chemical structures, and bioactivity data FAIR (Findable, Accessible, Interoperable, and Reusable). It notes that while small molecules that modulate biological systems are fundamental to fields like drug discovery, vast amounts of data about compounds (C), assays (A), results (R), and targets (P) remain trapped in PDFs. For data to be maximally useful, the relationships between these elements (D-A-R-C-P chains) need to be captured and linked in open databases. However, current methods of data extraction from journals are insufficient, and full automated extraction of D-A-R-C-P relationships is still a long way off
Connectivity > documents > structures > bioactivity
This document provides an overview of connectivity between chemistry, biology, and published documents. It discusses the challenges of extracting this information ("D-A-R-C-P") from publications and patents. While some commercial and open-source efforts curate this data, most of it remains buried in documents. Automated extraction has limitations compared to expert curation. The document argues that authors should directly connect their results to databases to improve flow of information.
Peptide tribulations
Presented to David Gloriam's Group, Copenhagen, Feb 2020
**********************************
The theme will be presented from the perspective of both past involvement in peptide curation in the Guide to Pharmacology (GtoPdb) and in current searching for bioactive peptides in the wider ecosystem that includes ChEMBL and PubChem. The core problem is that peptides hang in limbo land between bioinformatics (BLAST) and cheminformatics (Tanimoto) neither of which provide optimal searching. Curating peptides in GtoPdb presents many challenges, including mapping endogenous peptides to Swiss-Prot cleavage annotations. For synthetic peptides, equivocal specification of modifications and exact positions of radiolabels are also problematic However, target-mapped citation-supported quantitative binding parameters are curated where possible. For those peptides falling below the PubChem CID SMILES limit of approximately 70 residues, GtoPdb has been using Sugar and Splice from NextMove Software to convert into CIDs. Specific problems associated with finding bioactive peptides in databases will be outlined.
Vicissitudes of target validation for BACE1 and BACE2
Introduction/Background & Aims
The beta-amyloid (APP) cleaving enzyme (BACE1) was implicated as a drug target for Alzheimer's Disease (AD) back in 1999. In 2011, the paralogue, BACE2, became a new proposed target for type II diabetes (T2DM) having been reported to be the TMEM27 secretase regulating pancreatic beta-cell function [1]. By 2019 the accumulated evidence, including a swathe of failed clinical trials for BACE1 inhibitors, has produced a de facto de-validation of both targets in both diseases. As a learning exercise, the series of events leading up to this is reviewed here.
Method/Summary of work
Basic information about these two targets and the lead compounds against them were sourced via the IUPHAR/BPS Guide to Pharmacology (GtoPdb) as Target ids: 2330 and 2331, for BACE1 and 2, respectively. This was consolidated by a literature and patent review as well as following them in other databases. The most recent information on clinical trials was sourced from press releases.
Results/Discussion
GtoPdb annotates 24 lead compounds against BACE1 and 12 against BACE2. The corresponding counts mapped to these targets in ChEMBL are 8741 and 1377 making BACE1 one of the most actively pursued enzyme targets ever. Notwithstanding the massive global effort during 2018 Merck’s verubecestat and J&J’s atabecestat BACE1 inhibitors not only failed their Phase III endpoints but even appeared to worsen cognition in prodromal patients. In 2019 Amgen/Novartis stopped Phase II/III trials of umibecestat that also showed more cognitive decline in the treatment group compared to controls. BACE2 presented an anomalous situation in several ways. By 2016 both Novartis and Amgen declared their inability to reproduce the TMEM27 secretase turnover reported in 2011. Notwithstanding, Novartis and other companies have published patents on BACE2-specific inhibitors over several years and paradoxically verubecestat is more potent against BACE2 rather than 1 but was never tested for glucose-lowering. Equally puzzling is that one academic group is still publishing BACE2 inhibitors for T2D even post de-validation. One thing both targets have in common is the complete absence of genetic support from genome-wide disease association studies but this warning sign went unheeded.
Conclusions
The massive waste of resources on the pursuit of BACE1 as an AD target over the last two decades is catastrophic. This tale of de-validation is compounded for this paralogous pair of enzymes by the fact that the original evidence for BACE2 as a T2D target was eventually refuted. The story of these targets highlights a range of crucial pharmacological pitfalls that must be avoided in the future.
Reference(s)
[1] Southan C, Hancock J.M. (2013) A tale of two drug targets: the evolutionary history of BACE1 and BACE2. Front Genet. 4:293.
Guide to Pharmacology database: ELIXIR updae
The document describes several pharmacology databases and resources maintained by IUPHAR/BPS including:
1) The Guide to PHARMACOLOGY database which contains drug targets, ligands, and approved drugs. It is updated quarterly and accessible online.
2) The Guide to MALARIA PHARMACOLOGY database which contains information on antimalarial compounds and their molecular targets.
3) Efforts to add semantic mark-up and link entities between pharmacology databases and other resources like ChEMBL, PubChem, and UniProt to improve interoperability.
In silico 360 Analysis for Drug Development
Introduction:
Consequent to a memorandum of understanding between the Karolinska Institutet and the International Union of Basic and Clinical Pharmacology (IUPHAR) in 2018 a report on academic drug development, including guidelines (ADEV) has been drafted [1]. As part of this exercise, we conceived a triage for comprehensive informatics profiling around the compound, target, disease axis. We have termed this “in slico 360” (INS360) the aim of which was to support ADEV teams since they may lack either internal expertise or external support to do this on their own. Indeed, some past SciLifeLab Drug Discovery and Development Platform projects had been halted because of overlooked competitive impingements or insufficient target validation evidence.
Methods
We assessed the current database landscape, mostly public but including commercial, for potential utility for INS360. We were guided primarily by content coverage, usability, and reputation. We also explored some open property prediction resources for assay interference and toxicological inferences.
Results:
As a first-stop-shop, we selected the IUPHAR/BPS Guide to PHARMACOLOGY with ~900 ligand-target relationships captured via expert curation of journal papers Moving up in scale we evaluated ChEMBL at 1.8 million compounds with 1.1 million assay descriptions and 7,000 targets. With yet another jump we could search the patent corpus with 18 million extracted compounds in SureChEMBL. We explored PubChem that integrates these three with over 500 other sources linked to 96 million compounds, BioAssay results and connectivity into the NCBI Entrez system. The final jump in scale for document-to-chemistry navigation was represented by SciFinder with 155 million structures. On the target side, 360-exploration has the need to encompass literature, structure, genetic variation, splicing, interactions, and disease pathways. From their UniProt links, both GtoPdb and ChEMBL provide these entry points. Navigating genetic association data in support of target validation was enabled by the OpenTargets portal and the GWAS Catalog. We also fount servers that could produce prediction scores from chemical structures for a range of features important for de-risking development.
Conclusion:
This work scoped out initial resource choices for the INS360. We propose that not only ADEV operations but essentially any pharmacology research team has much to gain from this approach and many potential pitfalls can consequently be avoided when approaching key checkpoints, such as preparing a publication. However, support may be needed for both institutions and teams to get the best out of these complex and feature-rich databases.
[1] Southan C, (2019) Towards Academic Drug Development Guidelines, ChemRxiv pre-print no. 8869574
Will the correct BACE ORFs please stand up?
BACE1 and BACE2 are protease targets for Alzheimer's and diabetes, respectively but their validation is now questioned
Phylogenetic analysis can added functional insights
This came up against two key problems
A surprising prevalence of incorrect protein sequences predicted from genomes
Many BACE1 and BACE2 orthologues had truncation and/or indel errors.
Key phylogenetic representative genomes are languishing in an unfinished state
Some options for amelioration of these problems will be described
An update on the evolution of these enzymes will be shown
Desperately seeking DARCP
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.
5HT2A modulators update for SAFER
Look for new and potentially useful human 5HT2A-directed small molecule chemistry surfaced since the last meeting., check for compounds against as 5HT2A primary target but also combined inhibitors, poll round the key databases, literature and patents, earching challenges arise from synonym soup, complex cross-reactivities (see PMID 29679900) in vitro data gaps and in vivo polypharmacology
Quality and noise in big chemistry databases
Presented at Aug 2019 ACS by Antony Williams. Abstract: The internet has changed the way we access chemistry data as well as providing access to data that can quickly proliferate and becomes referenceable. Web access to chemical structures and their integration with biological data has become massively enabling with numbers for UniChem, PubChem and ChemSpider reaching 157, 97 and 71 million respectively (at the time of writing). A range of specialist databases small enough to be curated have stand-alone utility and synergies when integrated into the larger collections. These include DrugBank, BindingDB, ChEBI, and many others. Databases of any size have inherent quality challenges but at large scale various forms of “noise” accumulate to problematic levels. The unfortunate consequence is that “bigger gets worse”. This is particularly associated with large uncurated submissions from vendors and automated document extractions (even though these are high-value). Virtual enumerations and circularity between overlapping sources add to the problem. As a result of some of the noise in the larger databases the value becomes highly dependent on the specific applications. An example includes using the databases to support non-targeted analysis. This presentation covers examples of these noise and quality issues and suggests at least some options to ameliorate the problem
Connecting chemistry-to-biology
Progress in drug discovery and chemical biology is hugely enabled by curated document-assay-result-compound-target relationships (D-A-R-C-P) in open databases from resources such as the Guide to Pharmacology and ChEMBL. These are synergistically integrated into PubChem which pre-computes chemical similarity and connectivity between over 95 million structures and 5.6 million BioAssay results. It also links chemistry to documents via various additional routes including MeSH and large scale submissions from publishers. However, these efforts are patchy and very few journals facilitate such connectivity. There thus remains a massive shortfall in public D-A-R-C-P capture from decades of papers and patents. This presentation will cover these aspects and discuss their partial amelioration by options such as author-driven depositions and open lab-book approaches as used by Open Source Malaria
GtoPdb June 2019 poster
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.
PubChem as a source of systems biology perturbagens
Presented at Centre for Integrative Systems Biology and Bioinformatics meeting at Imperial College London “Modelling Biological Systems” March 2019
PubChem for drug discovery and chemical biology
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.
Will the real proteins please stand up
Poster for BPS Pharmacology 2018, London https://www.bps.ac.uk/news-events/events/2018/december/pharmacology-2018
Peptide Tribulations
Presentation for BPS Pharmacology 2018, London https://www.bps.ac.uk/news-events/events/2018/december/pharmacology-2018
Looking at chemistry - protein - papers connectivity in ELIXIR
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
Guide to Immunopharmacology update
Presented at IMMUNOPHARMACOLOGY: challenges, opportunities and research tools, Edinburgh, Scotland, 1-2nd October 2018
Druggable Proteome sources in UniProt
This document summarizes and compares different sources of data on the druggable proteome, including the IUPHAR/BPS Guide to Pharmacology (GtoPdb), ChEMBL, DrugBank, BindingDB, and Swiss-Prot. It finds that these sources have some unique and overlapping protein targets. Only 3.4% of human proteins are covered by all four main sources. The document discusses expanding the druggable proteome through new modalities and probes, as well as challenges such as validation costs and reproducibility issues.
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Connectivity > documents > structures > bioactivity
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Vicissitudes of target validation for BACE1 and BACE2
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Seeking glimmers of light in Pharos “Tdark” proteins
Seeking glimmers of light in Pharos “Tdark” proteins
PubChem as a source of systems biology perturbagens
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Looking at chemistry - protein - papers connectivity in ELIXIR
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