Unifying the Identification of Biomedical Entities with the Bioregistry

¹

,

²

,

Gyori

³

2022

Preprint

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…by assigning more precise predicates and including provenance information). Second, we hope to see these resources converging on external standards for the syntax and semantics used to communicate the entities and predicates appearing in mappings, such as the Bioregistry (Hoyt et al ., 2022c) in order to improve interoperability. Third, we hope to see large-scale efforts to aggregate, store, and redistribute mappings with more general scope than existing mapping services.…”

Section: Discussionmentioning

confidence: 99%

“…The first step of the cycle comprises retrieval and preprocessing of target identifier resources, including any existing mappings between the resources. We automate this process for ontologies by using the Bioregistry (Hoyt et al ., 2022c) to locate the ontology (i.e., with a URL) and ROBOT (Jackson et al ., 2019) to parse it. Similarly, we use custom automated preprocessing workflows in PyOBO (Hoyt et al ., 2022b) for other identifier resource types (e.g., databases like HGNC).…”

Section: Methodsmentioning

confidence: 99%

“…Second, it uses GitHub as technical platform to host and distribute the project’s code and data openly and as a social platform to enable discussion and external contribution through pull requests. Third, it uses GitHub Actions as a continuous integration and continuous delivery system to apply data quality checks (e.g., all mappings’ prefixes and local unique identifiers are compliant with the Bioregistry (Hoyt et al ., 2022c)). Further, several summaries (e.g., charts, tables, website), analyses (see Section 2.4.2), and artifacts (see Section 3.1) are automatically re-generated when a pull request is merged and archived on Zenodo (Hoyt et al ., 2022a).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Prediction and Curation of Missing Biomedical Identifier Mappings with Biomappings

¹

,

²

,

Gyori

³

2022

Preprint

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…Additionally, some PX resources have their own identifiers for datasets, that can also be used in parallel to the PXD identifiers. Furthermore, Digital Object Identifiers (DOIs) can also be issued for ‘Complete’ submissions (see below for more details about submission types) and PXD identifiers are resolved by the identifier resolution services identifiers.org ( 15 ) and Bioregistry ( 16 ). In terms of data license, all PX resources moved to a default Creative Commons CC0 license as the basis in 2020.…”

Section: Current Px Data Workflow and Implementation Of Psi Data Stan...mentioning

confidence: 99%

The ProteomeXchange consortium at 10 years: 2023 update

Deutsch

¹

,

Bandeira

²

,

Pérez‐Riverol

³

et al. 2022

Nucleic Acids Research

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.

“…Where possible, SeMRA wraps preexisting parsers for standard representations. For instance, SeMRA reads mappings from ontologies in OBO format by wrapping the PyOBO Python package [29]. Similarly, SeMRA reads mappings from ontologies in the OWL and OBO Graph JSON formats using the Bioontologies Python package [25].…”

Section: Sourcesmentioning

confidence: 99%

Assembly and reasoning over semantic mappings at scale for biomedical data integration

¹

,

Karis

²

,

Gyori

³

2025

Preprint

Self Cite

0

Exaggerated anticipatory anxiety is common in social anxiety disorder (SAD). Neuroimaging studies have revealed altered neural activity in response to social stimuli in SAD, but fewer studies have examined neural activity during anticipation of feared social stimuli in SAD. The current study examined the time course and magnitude of activity in threat processing brain regions during speech anticipation in socially anxious individuals and healthy controls (HC). Method Participants (SAD n = 58; HC n = 16) underwent functional magnetic resonance imaging (fMRI) during which they completed a 90s control anticipation task and 90s speech anticipation task.