Data · dataset · 2019
Application and evaluation of automated semantic annotation of gene expression experiments
Listed in Borealis and Agri-environmental Research Data Dataverse — shown once because both records carry DOI 10.5683/sp2/nvboaz
MOTIVATION: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values.
Description
Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets.
RESULTS: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments.
Read the rest (4 more)
We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references.
The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise.
We have integrated this annotation pipeline into Gemma. AVAILABILITY: The source code, documentation and Supplementary Materials are available at chibi.ubc.ca/GEOMMTX. The results of the manual evaluations are provided as Supplementary Material.
Both manual and predicted annotations can be viewed and searched via the Gemma website at chibi.ubc.ca/Gemma. The complete set of predicted annotations is available as a machine readable resource description framework graph.
Links
Where it is published
- Dataverse dataset page borealisdata.ca/dataset.xhtml?persistentId=doi%3A10.5683%2FSP2%2FNVBOAZ ↗
landing page · from borealisdata ca
- DOI doi.org/10.5683/sp2/nvboaz ↗
DOI / persistent id · from borealisdata ca
Catalogue records · 1
- Dataverse API borealisdata.ca/api/datasets/:persistentId/?persistentId=doi%3A10.5683%2FSP2%2… ↗
metadata API · from borealisdata ca
Topics
- Stated by source
- Medicine, Health and Life Sciences · Medicine, Health and Life Sciences
- From keywords
- Chemistry · Computer Science & AI · Earth & Environmental Science · Economics & Finance · Engineering · Humanities · Life Sciences · Life Sciences · Mathematics & Statistics · Medicine & Health · Medicine & Health · Ocean & Atmospheric Science · Social Science
- Inferred from text
- Gene expression 79% · Text 75%
Provenance · 2 source records, 23 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Borealis | doi:10.5683/SP2/NVBOAZ | 11 d ago | JSON v1 |
| Agri-environmental Research Data Dataverse | doi:10.5683/SP2/NVBOAZ | 10 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:field:310505 | enrichment · borealisdata ca | taxonomy-embedding@1.0.0 | title+keywords+description (79%) |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /subjects |
| concepts[field].dataverse_subject:medicine-health-and-life-sciences | source · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:chemistry | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:computer-science-ai | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:earth-environmental | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:economics-finance | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:engineering | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:humanities | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · borealisdata ca | connector:borealisdata_ca@1.0.0 | /subjects |
| concepts[field].local:field:life-sciences | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:mathematics-statistics | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:medicine-health | mapping · borealisdata ca | connector:borealisdata_ca@1.0.0 | /subjects |
| concepts[field].local:field:ocean-atmospheric | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[field].local:field:social-science | mapping · borealisdata ca dataverse | connector:borealisdata_ca_dataverse@1.0.0 | /subjects |
| concepts[modality].local:modality:text | enrichment · borealisdata ca | keyword-concept-rules@1.0.0 | title+description (75%) |
| created_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| description | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /description |
| publication_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| title | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | /name |
| updated_date | source · borealisdata ca | connector:borealisdata_ca@1.0.0 | |
| version_label | source · borealisdata ca | connector:borealisdata_ca@1.0.0 |