IndraLab

Statements

CALM1 binds GO. 77 / 77
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"Finally, the Gene Ontology Causal Activity Models (GO-CAM, [44]) consists of pathways annotated (manually or computationally) with the Gene Ontology (GO) terminology [45] (i.e. with GO terms describing biological processes, molecular functions and cellular components)."
33378765
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"Each GO-CAM model is represented using the Web Ontology Language (OWL), which is converted computationally to standard GO annotations (GAF format), ensuring backward compatibility."
30395331
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"GO-CAM is robust in terms of computational aspects: OWL is a powerful representation that structures knowledge in a way that allows for reasoning and offers the potential for real-time consistency checking during a curation process."
33378765
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"GO-CAM are models of biological systems and pathways that are generated by linking together multiple GO annotations in a semantically structured manner using the Relation Ontology (Smith et al. xref )."
34698891
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"The explicit relationship between the molecular function, biological process, and cellular component of each gene function is also defined by GO-CAM."
32962098
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"GO-CAM models center on molecular functions that are part of a biological process, which in turn are part of regulatory or signaling networks."
31840793
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"The new GO-CAM curation encourages the annotation of biological pathways, with relations between GO terms added for each step in the pathway (see xref )."
31840793
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"For example, the schema includes constraints that define allowable evidence and provenance structures for each assertion within a GO-CAM."
33290552
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"Causality between entities in a GO-CAM model is defined via building blocks of the form: ‘a molecular function, enabled by a gene product, regulates a molecular function, enabled by the same or another gene product’."
33378765
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"The GO-CAM documentation, data and download are directly accessible through."
33290552
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"Current formats of causal statements range from the simplest, with only two entities and the causal relationship [e.g. the Simple Interaction Format (SIF) with ‘A activates B’ or ‘A -> B’], to more complex statements including contextual description [e.g. BEL (Biological Expression Language) ( xref ; xref ), GO-CAM ( xref ) and PSI-MITAB2.8 ( xref )]."
32637990
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"We focus on our progress on the curation and public release of GO-CAM models, the continuous collaborative work to refine the GO ontology, the review and improvement of the quality of our annotations, and the expansion of the usability of GO through a redesigned website, documentation, data access, visualization widget and 15 years of historical archives of the GO knowledgebase."
33290552
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"GO-CAM, our new framework for defining and representing gene functions with more accuracy, consistency and precision, is being used to create a growing set of curated biological models, and we encourage the analysis tool developer community to explore the new format and potential new applications of these models."
30395331
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"We have implemented a computational schema for GO-CAM using ShEx (Shape Expressions), a formal language for describing structures in Resource Description Format (RDF) graphs (), also used in projects such as Wikidata ()."
33290552
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"GO-CAM is a strict semantic, descriptive and computable model that enables curators to link together standard GO annotations and enrich them with biological context."
33290552
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"GO-CAM repository."
33290552
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"GO-CAM models and associated tooling are gradually replacing the traditional GO annotation process within the Alliance for Genomic Resources ( xref ), meaning that future GO annotation will produce an increasingly rich, manually curated KG."
33954284
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"GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models."
30395331
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"By employing the Gene Ontology (GO) resources, we have performed a combination of standard GO annotations (GO-CAM) to produce a network between BM steady-state conditions VSELs (SSC-VSELS) and FSH + NAM expanded VSELs (FSH + NAM VSELs)."
35986128
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"Federated queries allow, for instance, to query features of a GO-CAM and enrich these features with additional information available at other SPARQL endpoints such as UniProt (), identifiers.org () and wikipathway ()."
33290552
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"In parallel, the development of GO-CAM models has been useful in identifying inconsistent annotation practices, and has provided opportunities to develop consortium-wide annotation guidelines."
30395331
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"Second, the new gene product–GO term relations form part of the Gene Ontology Causal Activity Modelling (GO-CAM) [ xref ] system, which uses OWL to represent how the molecular activities of gene products interconnect to carry out, and regulate, biological processes."
32875947
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"In theory, PSI-MITAB2.8, BEL and GO-CAM can also be used as input files in modeling tools when the interactions of interest have been selected."
33378765
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"The Gene Ontology Consortium, with the development of the Causal Activity Model (GO-CAM), now provides a mechanism to express this type of information ( xref )."
35295568
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"Multiple standard GO annotations are linked to larger models of biological functions by GO-CAM in a semantically structured manner."
32962098
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"To make functional annotations using the Gene Ontology even more useful for representing biological systems, MGD curators have been working with the Gene Ontology Consortium to develop Causal Activity Models based on GO (GO-CAM) (Thomas et al. xref )."
34698891
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"SynGO annotations are available as both standard GO annotations () and as GO-CAM models ()."
31171447
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"For example, high-throughput experiments for gene expression generate hundreds or sometimes thousands of differentially expressed genes (DEGs), and their associated biological functions can be summarized through enrichment analysis over GO terms. xref Gene-level annotations defined in GO can also be further elaborated into a network of biological pathway annotations via the recently developed GO Causal Activity Modeling (GO-CAM) models to represent the integrative effect of DEGs on the level of biological pathways."
32939051
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"We continue to develop Noctua, the new GO curation platform (see GO toolset), to support the curation and review of both standard and GO-CAM annotations."
33290552
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"To address this and to help curators, the Noctua annotation platform is being developed (http://noctua.geneontology.org/), providing a graphical user interface for assembling, editing and interpretation of GO-CAM models."
33378765
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"In addition, we ingest GO Causal Activity Models (GO-CAM) models that capture biological systems such as protein pathways, including those important in SARS-CoV-2 infection(Thomas et al., 2019). generate positive edges, a set of positive test edges equal in number to [(1 -train_fraction) * number of edges in input graph] is selected from the edges in the input graph, where train_fraction is a number between 0 and 1 indicating the fraction of the graph to use for training."
33196056
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"For example, the Gene Ontology Causal Activity Modeling (GO-CAM) will enable new applications of GO in pathway and network analysis [ xref ]."
32598315
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"On the other hand, GO-CAM and BEL allow the representation of causality from an activity-based view for the biological entities, and a process-based view for biological reactions, meaning that the focus is not put on biological entities per se but rather on functions or actions that they can perform."
33378765
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"The GO-CAM ShEx schema plus associated documentation is available from."
33290552
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"GO-CAM specifies the semantics of GO annotations, and how standard GO annotations can be combined into a larger model."
30395331
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"In addition, we have initiated a phased project to migrate all standard manual GO annotations generated by Alliance member groups to GO-CAM starting with WormBase ( xref ) and MGI ( xref )."
33290552
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"Hence, a model concept called GO Causal Activity Modeling (GO-CAM) was introduced in 2018 to extend the existing annotation to represent a complex statement that can be scalable and structured [ xref ]."
32962098
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"The ongoing “Causal Activity Model” project (GO-CAM; [ xref ]) is going one step further in expressiveness with the design of refined properties between GO-BP and GO-MF."
| PMC
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"Users can now access the GO-CAM repository directly from the GO homepage."
33290552
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"In this study, we explored whether the GO-CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode C. elegans (C. elegans Neural Circuit Causal Activity Modelling (CeN-CAM))."
37162850
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"The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology Causal Activity Modelling, or GO-CAM)."
37162850
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"GO-CAM alleviates this problem, by connecting gene function to activators, substrates, and larger processes."
35295568
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"GO-CAM is based on the GO terminology and uses the Relation Ontology (RO) terms for the annotation of causal interactions [95]."
33378765
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"Some other MAPK processes such as ‘GO:1903616 MAPK cascade involved in axon regeneration’ will eventually be obsoleted, as these combine two or more other GO terms and can be composed in GO-CAM."
30395331
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"The GO is currently rapidly increasing the curation of GO-CAM models, and the model repository is growing."
30395331
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"A paper detailing GO-CAM is in preparation, but we summarize some properties here."
30395331
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"We refer to the framework as GO- C ausal A ctivity M odeling (GO-CAM, formerly referred to as ‘LEGO’ ( xref )) and to GO-CAMs as models to distinguish them from standard annotations ."
30395331
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"The introduction of Causal Activity Modelling (GO-CAM) [ xref ] tries to address this issue and to unify GO terms by using causal graphs to model their interrelations."
33120976
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"Other resources such as GO-CAM and NDEx represent new developments that aim to propel component and network curation results to new future applications and are probably safe for some time to be."
33378765
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"These formats can range from the simplest form with two entities and the regulation sign (e.g. SIF) and more complex representations with the storage of additional metadata [e.g. the BEL, GO-CAM using the Web Ontology Language (OWL), and PSI-MITAB]."
33378765
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"For example, genes or proteins can also be viewed as part of the GO-CAM causal graph, thereby transforming the AFP problem into a semi-supervised learning problem of predicting new edges in that graph, specifically edges connecting the genes with the terms."
33120976
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"The recent development of GO-CAM models [ xref ] and our collaboration with them to export Reactome reaction annotations into GO-CAM format helps to bridge this knowledge gap."
32486891
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"More recently, the GO consortium has moved to ‘Causal activity modeling (GO-CAM)’, a more complete way of representing the biological function of a gene by connecting the individual GO annotations in order to describe networks or pathways ( xref )."
32559296
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"The biggest change has been in biological process terms, due to refactoring the multi-organism part of the Biological Process branch and the obsoletion of combinatorial terms (e.g. GO:0100052, negative regulation of G1/S transition of mitotic cell cycle by transcription from RNA polymerase II promoter) made up of other GO terms which can now be linked using GO-CAM."
33290552
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"The GO-CAM [44] is a formalism developed for structuring biological processes by defining triplets of information (subject, predicate and object) using the OWL representation [94]."
33378765
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"In GO-CAM, each model is represented as a set of triples ( subject - relation -object, with brackets {} as a set container), e.g. { ABCA1 enables cholesterol transporter activity ; cholesterol transporter activity occurs in plasma membrane , and cholesterol transporter activity part_of cholesterol homeostasis}."
30395331
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"26 In addition, we ingest GO-CAM models that capture biological systems such as protein pathways, including those important in SARS-CoV-2 infection."
| DOI
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"The establishment of these guidelines encourages the communities to update data formats (PSI-MITAB2.8, GO-CAM and BEL) and curation protocols to comply with MI2CAST and offer better interoperability between resources supporting these formats."
33378765
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"Users will be able to access and merge these data using the MITAB2.8-compliant PSICQUIC webservice ( xref ). xref provides the compliance to MI2CAST of several formats (SIF, PSI-MITAB2.8, BEL and GO-CAM)."
32637990
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"Incorporating the ‘grammar’ of GO-CAM relations into prediction models will also be an interesting challenge."
33120976
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"These annotations were also deposited in the Gene Ontology annotation repository () as GO-CAM models ( xref )."
31171447
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"The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs."
33290552
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"Still, GO-CAM is mainly based on an activity-level or reaction-level representation of causality rather than an entity-level based causality (even though the latter can be inferred)."
33378765
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"Thus, the GO consortium has recently implemented the Gene Ontology Causal Activity Model (GO-CAM; xref ) to allow the representation of comprehensive models of biological pathways."
31840793
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"GO-CAM is an extension of the standard GO annotation format that allows more expressive annotations, e.g. specifying the cell type using Cell Ontology terms ( xref ), and multiple pieces of evidence for a single annotation."
31171447
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"All other upstream and downstream molecular functions/biological processes will be modeled in GO-CAM with causal relationships between them and the MAPK cascade."
30395331
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"GO-CAM in a nutshell."
33290552
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"dictyBase and other curators use a new tool created by the GO consortium (Noctua), to accomplish these GO-CAM annotations."
31840793
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"Other resources, such as GO-CAM, focus not on the genes, but on the biological activities of gene products, and represent these activities as being the source and target ‘entities’ of the causal interaction (see Figure 2, Example 2), therefore called ‘activity-based causality’."
33378765
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"Over 300 GO-CAM models are currently available for mouse currently ()."
34698891
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"In parallel, the Gene Ontology [GO ( xref )], since 2003, has included a ‘regulation of biological process’ (GO:0050789) branch that has been widely used to annotate causal interactions ( xref ), and has recently been extended into the GO Causal Activity Models (GO-CAM) framework ( xref )."
32637990
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"The migrated standard GO annotations are also being checked against the ShEx schema to ensure compliance with the GO-CAM model."
33290552
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"The GO-CAM formalism thus enables queries such as ‘which genes’ activities are upstream or downstream of a given activity or process’ or ‘which genes’ activities directly positively regulate a given activity’."
33290552
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"Furthermore, BEL, GO-CAM and PSI-MITAB2.8 allow to depict with precision the biological activities of the entities involved, using GO terms."
33378765
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"For storing any type of contextualized causal interactions, the PSI-MITAB2.8, BEL and GO-CAM formats seem to be well suited as they can handle fine-grained details describing a causal interaction."
33378765
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"In molecular biology, several formalisms (e.g., BEL,87 SBML,182 SBGN,183 BioPAX,184 GO-CAM)185 have the facility to describe the interactions between biological entities that are often elucidated through laboratory or clinical experimentation."
34553169
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"MI2CAST considers terms used in formats mentioned previously (e.g. PSI-MITAB2.8, BEL and GO-CAM) and covers the full range of metadata that should ideally be annotated during the curation process to enrich the description of a molecular causal interaction."
32637990