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Book ; Thesis: Einfluss des Serotoninagonisten m-Chlorophenylpiperazin (mCPP) auf Befindlichkeit und Vitalparameter bei gesunden männlichen Probanden

Stephan, Ralf

2003

Author's details	vorgelegt von Ralf Stephan
Language	German
Size	63 S. : graph. Darst.
Publishing country	Germany
Document type	Book ; Thesis
Thesis / German Habilitation thesis	Bonn, Univ., Diss., 2003
HBZ-ID	HT013890455
Database	Catalogue ZB MED Medicine, Health

In stock of ZB MED Cologne/Königswinter

Shelf mark	Loan status	Location
2003 D 2741	order for loan	Magazin

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Article: ChatGPT usage in the Reactome curation process.

Tiwari, Krishna / Matthews, Lisa / May, Bruce / Shamovsky, Veronica / Orlic-Milacic, Marija / Rothfels, Karen / Ragueneau, Eliot / Gong, Chuqiao / Stephan, Ralf / Li, Nancy / Wu, Guanming / Stein, Lincoln / D'Eustachio, Peter / Hermjakob, Henning

bioRxiv : the preprint server for biology

2023

Abstract: Appreciating the rapid advancement and ubiquity of generative AI, particularly ChatGPT, a chatbot using large language models like GPT, we endeavour to explore the potential application of ChatGPT in the data collection and annotation stages within the ... ...

Abstract	Appreciating the rapid advancement and ubiquity of generative AI, particularly ChatGPT, a chatbot using large language models like GPT, we endeavour to explore the potential application of ChatGPT in the data collection and annotation stages within the Reactome curation process. This exploration aimed to create an automated or semi-automated framework to mitigate the extensive manual effort traditionally required for gathering and annotating information pertaining to biological pathways, adopting a Reactome "reaction-centric" approach. In this pilot study, we used ChatGPT/GPT4 to address gaps in the pathway annotation and enrichment in parallel with the conventional manual curation process. This approach facilitated a comparative analysis, where we assessed the outputs generated by ChatGPT against manually extracted information. The primary objective of this comparison was to ascertain the efficiency of integrating ChatGPT or other large language models into the Reactome curation workflow and helping plan our annotation pipeline, ultimately improving our protein-to-pathway association in a reliable and automated or semi-automated way. In the process, we identified some promising capabilities and inherent challenges associated with the utilisation of ChatGPT/GPT4 in general and also specifically in the context of Reactome curation processes. We describe approaches and tools for refining the output given by ChatGPT/GPT4 that aid in generating more accurate and detailed output.
Language	English
Publishing date	2023-11-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.08.566195
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book: Im Mähdrusch Kosten senken

Stephan, Ralf

(Bauernzeitung ; Entscheidungshilfen für Fach- und Führungskräfte ; 2003,2)

2003

Author's details	[Red.: Ralf Stephan]
Series title	Bauernzeitung Entscheidungshilfen für Fach- und Führungskräfte ; 2003,2
Language	German
Size	43 S, Ill., graph. Darst, 30 cm
Publisher	Dt. Bauernverl
Publishing place	Berlin
Document type	Book
Database	Johann Heinrich von Thünen-Institut, Federal Research Institute for Rural Areas, Forestry and Fisheries

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Article ; Online: Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.

Database : the journal of biological databases and curation

2024 Volume 2024

Abstract: Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting changes to ... ...

Abstract	Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting changes to normal biology. A disease reaction is defined as an aberrant reaction in which a variant protein participates. A disease pathway is defined as a pathway that contains a disease reaction. Annotation of disease variants as participants of disease reactions and disease pathways can provide a standardized overview of molecular phenotypes of pathogenic variants that is amenable to computational mining and mathematical modeling. Reactome (https://reactome.org/), an open source, manually curated, peer-reviewed database of human biological pathways, in addition to providing annotations for >11 000 unique human proteins in the context of ∼15 000 wild-type reactions within more than 2000 wild-type pathways, also provides annotations for >4000 disease variants of close to 400 genes as participants of ∼800 disease reactions in the context of ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, described in wild-type reactions and pathways, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Reactome's data model enables mapping of disease variant datasets to specific disease reactions within disease pathways, providing a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity. Database URL: https://reactome.org/.
MeSH term(s)	Humans ; Phenotype ; Molecular Sequence Annotation ; Databases, Genetic ; Disease/genetics
Language	English
Publishing date	2024-05-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baae031
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The LOTUS initiative for open knowledge management in natural products research.

Rutz, Adriano / Sorokina, Maria / Galgonek, Jakub / Mietchen, Daniel / Willighagen, Egon / Gaudry, Arnaud / Graham, James G / Stephan, Ralf / Page, Roderic / Vondrášek, Jiří / Steinbeck, Christoph / Pauli, Guido F / Wolfender, Jean-Luc / Bisson, Jonathan / Allard, Pierre-Marie

eLife

2022 Volume 11

Abstract: Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and ... ...

Abstract	Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.
MeSH term(s)	Biological Products ; Computational Biology ; Databases, Factual ; Knowledge ; Knowledge Management
Chemical Substances	Biological Products
Language	English
Publishing date	2022-05-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.70780
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Using the Reactome Database.

Rothfels, Karen / Milacic, Marija / Matthews, Lisa / Haw, Robin / Sevilla, Cristoffer / Gillespie, Marc / Stephan, Ralf / Gong, Chuqiao / Ragueneau, Eliot / May, Bruce / Shamovsky, Veronica / Wright, Adam / Weiser, Joel / Beavers, Deidre / Conley, Patrick / Tiwari, Krishna / Jassal, Bijay / Griss, Johannes / Senff-Ribeiro, Andrea /

Brunson, Timothy / Petryszak, Robert / Hermjakob, Henning / D'Eustachio, Peter / Wu, Guanming / Stein, Lincoln

Current protocols

2023 Volume 3, Issue 4, Page(s) e722

Abstract: Pathway databases provide descriptions of the roles of proteins, nucleic acids, lipids, carbohydrates, and other molecular entities within their biological cellular contexts. Pathway-centric views of these roles may allow for the discovery of unexpected ... ...

Abstract	Pathway databases provide descriptions of the roles of proteins, nucleic acids, lipids, carbohydrates, and other molecular entities within their biological cellular contexts. Pathway-centric views of these roles may allow for the discovery of unexpected functional relationships in data such as gene expression profiles and somatic mutation catalogues from tumor cells. For this reason, there is a high demand for high-quality pathway databases and their associated tools. The Reactome project (a collaboration between the Ontario Institute for Cancer Research, New York University Langone Health, the European Bioinformatics Institute, and Oregon Health & Science University) is one such pathway database. Reactome collects detailed information on biological pathways and processes in humans from the primary literature. Reactome content is manually curated, expert-authored, and peer-reviewed and spans the gamut from simple intermediate metabolism to signaling pathways and complex cellular events. This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, worm, and other model organisms. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Browsing a Reactome pathway Basic Protocol 2: Exploring Reactome annotations of disease and drugs Basic Protocol 3: Finding the pathways involving a gene or protein Alternate Protocol 1: Finding the pathways involving a gene or protein using UniProtKB (SwissProt), Ensembl, or Entrez gene identifier Alternate Protocol 2: Using advanced search Basic Protocol 4: Using the Reactome pathway analysis tool to identify statistically overrepresented pathways Basic Protocol 5: Using the Reactome pathway analysis tool to overlay expression data onto Reactome pathway diagrams Basic Protocol 6: Comparing inferred model organism and human pathways using the Species Comparison tool Basic Protocol 7: Comparing tissue-specific expression using the Tissue Distribution tool.
MeSH term(s)	Humans ; Animals ; Mice ; Rats ; Metabolic Networks and Pathways ; Zebrafish/metabolism ; Databases, Protein ; Proteins/metabolism ; Signal Transduction
Chemical Substances	Proteins
Language	English
Publishing date	2023-04-13
Publishing country	United States
Document type	Journal Article
ISSN	2691-1299
ISSN (online)	2691-1299
DOI	10.1002/cpz1.722
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.

bioRxiv : the preprint server for biology

2023

Abstract: Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome, an open ... ...

Abstract	Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome, an open source, manually curated, peer-reviewed database of human biological pathways, provides annotations for over 4000 disease variants of close to 400 genes in the context of ∼800 disease reactions constituting ∼400 disease pathways. Functional annotation of disease variants proceeds from normal gene functions, through disease variants whose divergence from normal molecular behaviors has been experimentally verified, to extrapolation from molecular phenotypes of characterized variants to variants of unknown significance using criteria of the American College of Medical Genetics and Genomics (ACMG). Reactome's pathway-based, reaction-specific disease variant dataset and data model provide a platform to infer pathway output impacts of numerous human disease variants and model organism orthologs, complementing computational predictions of variant pathogenicity.
Language	English
Publishing date	2023-10-21
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.18.562964
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Reactome Pathway Knowledgebase 2024.

Nucleic acids research

2023 Volume 52, Issue D1, Page(s) D672–D678

Abstract: The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordered ... ...

Abstract	The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Here we review progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways. Finally, we briefly discuss issues involved in making Reactome more fully interoperable with other related resources such as the Gene Ontology and maintaining the resulting community resource network.
MeSH term(s)	Humans ; Knowledge Bases ; Metabolic Networks and Pathways/genetics ; Proteome/genetics ; Signal Transduction
Chemical Substances	Proteome
Language	English
Publishing date	2023-11-08
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad1025
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1067: Show issues

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bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Conference proceedings: The LOTUS initiative for knowledge sharing in Natural Products research

Rutz, Adriano / Sorokina, Maria / Galgonek, Jakub / Mietchen, Daniel / Willighagen, Egon / Gaudry, Arnaud / Graham, James G. / Stephan, Ralf / Page, Roderic / Vondrášek, Jiří / Steinbeck, Christoph / Pauli, Guido F. / Wolfender, Jean-Luc / Bisson, Jonathan / Allard, Pierre-Marie

Planta Medica

2021 Volume 87, Issue 15

Event/congress	GA - 69th Annual Meeting 2021, Virtual conference, Bonn, Germany, 2021-09-05
Language	English
Publishing date	2021-12-01
Publisher	Georg Thieme Verlag
Publishing place	Stuttgart ; New York
Document type	Article ; Conference proceedings
ZDB-ID	123545-x
ISSN	1439-0221 ; 0032-0943
ISSN (online)	1439-0221
ISSN	0032-0943
DOI	10.1055/s-0041-1736777
Database	Thieme publisher's database

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Uf I Zs.157: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article: Das Zusammenwachsen der Rentenversicherungen in West und Ost: eine Zwischenbilanz im zehnten Jahr der Deutschen Einheit

Stephan, Ralf-Peter

Die Angestellten-Versicherung : Zeitschrift der Bundesversicherungsanstalt für Angestellte ; amtliches Veröffentlichungsblatt Vol. 46, No. 12 , p. 546-556

1999 Volume 46, Issue 12, Page(s) 546–556

Author's details	von Ralf-Peter Stephan
Keywords	Gesetzliche Rentenversicherung ; Alte Bundesländer ; Neue Bundesländer ; Deutschland
Language	German
Publisher	Bundesversicherungsanstalt
Publishing place	Berlin
Document type	Article
ZDB-ID	279-3
Database	ECONomics Information System

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