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4 results for “annotation curation”
A Curated Gene and Biological System Annotation of Adverse Outcome Pathways Related to Human Health
<p>Adverse Outcome Pathways (AOPs) are multi-scale models of biological mechanisms connecting molecular initiating events to adverse outcomes through measurable key events. AOPs can guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation in chemical safety assessment. Here, we present a comprehensive molecular annotation of AOPs relevant to human health to embed the AOP framework into molecular data interpretation, which supports the development and application of novel AOP-based approaches in biomedical research.</p> <p>Please cite the following publication alongside this Zenodo entry when using the data:</p> <p>Saarimäki, L.A., Fratello, M., Pavel, A. <em>et al.</em> A curated gene and biological system annotation of adverse outcome pathways related to human health. <em>Sci Data</em> <strong>10</strong>, 409 (2023). https://doi.org/10.1038/s41597-023-02321-w</p>
Database of 16S sequences from SILVA (r114), filtered, curated and annotated to be used easily by programs of taxonomic assignments
<p>The database used for the taxonomic assignment of reads generally comes from the SILVA database (http://www.arb-silva.de/). The logic behind this database is to use the information from the best one to the worst one. This is why the curated database was splitted in two parts : the [C] sequences for Complete sequences in terms of taxonomy, and the [I] and [E] sequences, for Incomplete and Environmental sequences.</p> <p>Each sequence included into the database must have a specific format summarizing all needed information (example below):<br> >[I]AACY020336309;Archaea(superkingdom);Euryarchaeota(phylum);Thermoplasmata(class);Thermoplasmatales(order);Marine_Group_II(no_rank);;marine_metagenome</p> <p>This sequence is an incomplete one ([I]), with a specific accession number from NCBI or SILVA, or another database (AACY020336309). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, <br> class, order, family, and genus). The species name is the last one and separated by two ';' characters from the rest of the descriptive line. Finally, the descriptive line must not contain specific characters like spaces. If one or several levels are unknown, this is indicated by 'no_rank'.</p> <p>Another example here for [C] sequences:<br> >[C]AAAK03000010;Bacteria(superkingdom);Firmicutes(phylum);Bacilli(class);Lactobacillales(order);Enterococcaceae(family);Enterococcus(genus);;Enterococcus_faecium_DO<br> This sequence is a complete one ([C]), with a specific accession number from NCBI or SILVA, or another database (AACY020187844). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, <br> class, order, family, and genus). The species is the last one and separated by two ';' characters from the rest of the descriptive line. Complete sequences must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>Another example here for [E] sequences:<br> >[E]U59968;Archaea(superkingdom);Thaumarchaeota(phylum);Soil_Crenarchaeotic_Group(SCG)(no_rank);;uncultured_crenarchaeote<br> This sequence is a environmental one ([E]), with a specific accession number from NCBI or SILVA, or another database (U59968). Then, all taxonomic data is separated using ';' characters, for each considered level (superkingdom, phylum, class, order, family, and genus). The species is the last one and separated by two ';' characters from the rest of the descriptive line. Complete sequences <br> must have six levels of information (superkingdom, phylum, class, order, family, and genus). If it is not the case, the sequence will be considered as Incomplete ([I]) (between three and five levels), or Environmental ([E]) (with only the superkingdom and the phylum levels).</p> <p>More details on the steps defined to clean and define this new database can be available on demand (sebastien.terrat@inra.fr).</p>
Manually Curated Library of Transposable Elements (TEs) and TE Annotations for Drosophila amaguana
<p>This data collection provides a manually curated library of transposable elements (TEs) for <em>Drosophila amaguana</em>, including consensus sequences, genome-wide TE annotations, and individual TE copy sequences. The library was built using <em>de novo</em> generated by EDTA (Extensive <em>de novo</em> TE Annotator) and RepeatModeler, curated with MCHelper, and further processed for genome annotation using RepeatMasker and OneCodeToFindThemAll. </p> <p>Below is a description of the included files:</p> <ul> <li><strong><code>Dama_curated_TE_library.fasta</code>:</strong> Contains 737 consensus TE sequences manually curated for <em>D. amaguana</em>. Sequence identifiers include classification and origin (e.g., new families or similarity to known elements). The identifier for each sequence in the FASTA file includes information about its classification:<br><br> <ul> <li><strong>For sequences corresponding to potentially new families</strong>: The identifier consists of a three-letter abbreviation for <em>D. amaguana</em> (Dama), followed by the new family identifier and the superfamily name, all separated by underscores. <em>Example: </em>Dama_NF_BELPAO_1.</li> <li><strong>For consensus sequences that show similarity to TE sequences previously reported in other species</strong>: The identifier includes the abbreviation Dama, followed by the superfamily name and an abbreviation for the species in which the TE was previously reported, all separated by underscores. Example: Dama_Helitron-1_DVir.<br><br></li> </ul> </li> <li><strong><code>Dama_TE_annotations.out</code>:</strong> Genome-wide annotation file of TE insertions produced with RepeatMasker and post-processed using OneCodeToFindThemAll to merge fragmented elements.</li> <li><strong><code>Dama_TE_copies.fasta</code>: </strong>FASTA file containing the extracted sequences of all annotated TE copies from the <em>D. amaguana</em> genome.</li> <li><strong><code>TEcopies_sequences.sh</code>:</strong> Shell script used to extract TE copy sequences from the genome using the annotation coordinates.</li> <li><strong><code>Dynamics_Dama.ipynb</code>: </strong>Jupyter Notebook for the analysis of transposable element (TE) dynamics in<strong> </strong><em>D. amaguana.</em></li> </ul>
Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni)
GEO Series GSE300824. Ceratotherium simum simum. 8 samples. Type: Expression profiling by high throughput sequencing.
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