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opencc-by-4.0Oct 2022View details →

Figs 170–175. Heads, anterior views. 170. Eccoptopsis costaricensis Blake, 1966 in New World genera of Galerucinae Latreille, 1802 (tribes Galerucini Latreille, 1802, Metacyclini Chapuis, 1875, and Luperini Gistel, 1848): an annotated list and identification key (Coleoptera: Chrysomelidae)

Figs 170–175. Heads, anterior views. 170. Eccoptopsis costaricensis Blake, 1966, ♂. 171. E. costaricensis, ♀. 172. Oroetes flavicollis Jacoby, 1888, ♂. 173. Porechontes wilcoxi Blake, 1966. 174. Geethaluperus flavofemoratus (Jacoby, 1888) comb. nov. 175. Scelolyperus cyanellus (LeConte, 1865).

opencc-by-4.0Oct 2022View details →

Figs 127–135. Dorsal views. 127 in New World genera of Galerucinae Latreille, 1802 (tribes Galerucini Latreille, 1802, Metacyclini Chapuis, 1875, and Luperini Gistel, 1848): an annotated list and identification key (Coleoptera: Chrysomelidae)

Figs 127–135. Dorsal views. 127. Scelida nigricornis (Jacoby, 1888). 128. Androlyperus incisus Schaeffer, 1906. 129. Inbioluperus flowersi Clark, 1993. 130. Scelolyperus cyanellus (LeConte, 1865). 131. Lygistus streptophallus Wilcox, 1965. 132. Phyllobrotica limbata (Fabricius, 1801). 133. Microscelida viridipennis Clark, 1998. 134. Phyllobrotica sororia Horn, 1896. 135. Scelidacne andrewi Clark, 1998.

opencc-by-4.0Aug 2017View details →

Processed and annotated yeast gene expression data from yeast2 and ygs98 platforms

This dataset contains the following files: <ul> <li>yeast2_processed_rds.tar.gz - processed gene expression matrices from the yeast2 platform. The data is stored in binary R format (.rds).</li> <li>ygs98_processed_rds.tar.gz - processed gene expression matrices from the yeast2 platform. The data is stored in binary R format (.rds).</li> <li>yeast2-curated-annotations.txt - metadata for the yeast2 platform.</li> <li>ygs98-curated-annotations.txt - metadata for the ygs98 platform.</li> </ul>

Fig. 2 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist

Fig. 2. Biomes in the Horn of Africa following Fishpool & Evans (2001). SG = Sudan-Guinea Savanna biome (green); AH = Afrotropical Highlands biome (blue); SM = Somali-Masai biome (yellow).

Fig. 1 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist

Fig. 1. The National Regional State of Oromia (red) within Ethiopia and the Horn of Africa (boundaries after MapLibrary 2013).

Fig. 6 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist

Fig. 6. The White-tailed Swallow Hirundo megaensis Benson, 1942 is another endemic species to Oromia, restricted to the Borana and Guji zone (Photo: Kai Gedeon).

Fig. 5 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist

Fig. 5. The Ethiopian Bush-crow Zavattariornis stresemanni Moltoni, 1938 is restricted to the Borana zone in SE Oromia, with a total range of just 6000 km² (Photo: Kai Gedeon).

Fig. 4 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist

Fig. 4. The Black-fronted Francolin Pternistis castaneicollis atrifrons (Conover, 1930) exists in a small mountain range around Mega in southern Oromia (Borana zone). It shows a number of distinct features that may justify the split from P. castaneicollis (Photo: Kai Gedeon).

Fig. 3 in The birds (Aves) of Oromia, Ethiopia - an annotated checklist

Fig. 3. The National Regional State of Oromia covered by 1-degree-tetrads. For the bold-red framed tetrads the data on distribution of birds was taken from the distribution atlas of Ash & Atkins (2009).

opencc-by-4.0Aug 2017View details →

PHENICX-Anechoic: note annotations for Aalto anechoic orchestral database

PHENICX-Anechoic: denoised recordings and note annotations for Aalto anechoic orchestral database       Description   This dataset includes audio and annotations useful for tasks as score-informed source separation, score following, multi-pitch estimation, transcription or instrument detection, in the context of symphonic music.   This dataset was presented and used in the evaluation of:   M. Miron, J. Carabias-Orti, J. J. Bosch, E. Gómez and J. Janer, "Score-informed source separation for multi-channel orchestral recordings", Journal of Electrical and Computer Engineering (2016))"   On this web page we do not provide the original audio files, which can be found at the web page hosted by Aalto University. However, with their permission we distribute the denoised versions for some of the anechoic orchestral recordings:   Pätynen, J., Pulkki, V., and Lokki, T., "Anechoic recording system for symphony orchestra," Acta Acustica united with Acustica, vol. 94, nr. 6, pp. 856-865, November/December 2008.   For the intellectual rights and the distribution policy of the audio recordings in this dataset contact Aalto University, Jukka Pätynen and Tapio Lokki. For more information about the original anechoic recordings we refer to the web page and the associated publication [2]   We provide the associated musical note onset and offset annotations, and the Roomsim[3] configuration files used to generate the multi-microphone recordings [1].   The anechoic dataset in [2] consists of four passages of symphonic music from the Classical and Romantic periods. This work presented a set of anechoic recordings for each of the instruments, which were then synchronized between them so that they could later be combined to a mix of the orchestra. In order to keep the evaluation setup consistent between the four pieces, we selected the following instruments: violin, viola, cello, double bass, oboe, flute, clarinet, horn, trumpet and bassoon.   We created a ground truth score, by hand annotating the notes played by the instruments. The annotation process involved gathering the original scores in MIDI format, performing an initial automatic audio-to-score alignment, then manually aligning each instrument track separately with the guidance of a monophonic pitch estimation.   During the recording process detailed in [2], the gain of the microphone amplifiers was fixed to the same value for the whole process, which reduced the dynamic range of the recordings of the quieter instruments. This lead to problems with which we had to deal, in order to reduce the noise. In the paper we described the score-informed denoising procedure we applied to each track.   A complete description of the dataset and the creation methodology, including the generation of the multi-microphone recordings, is presented in [1].     Files included The “audio” folder contains the audio files for each instrument in a given source: sourcenumber.wav, where “source” can be either violin, viola, cello, double bass, oboe, flute, clarinet, horn, trumpet or bassoon and “number” corresponds to the each separated instrument in a given source (e.g. there are two violins in the “mozart” piece, thus you will find “violin1.wav” and “violin2.wav” in the “mozart” folder).   The “annotations” folder includes note onsets and offset annotations as MIDI and text files for the corresponding audio files in the dataset. The annotations are offered per source: source.txt and source.mid, where “source” can be either violin, viola, cello, double bass, oboe, flute, clarinet, horn, trumpet or bassoon. Additionally, for tasks as score-following, we provide MIDI which is not aligned with the audio as MIDI and text file: source_o.txt and source_o.mid. Furthermore, an additional MIDI file all.mid holds the tracks for all the sources in a single MIDI file. The text files comprise all the notes played by a source in the following format: Onset,Offset,Note name We recommend using the ground truth annotations from the text file as the MIDI might have problems due to the incorrect duration for some notes.   The “Roomsim” folder contains the configuration files (“Text_setups”) and the impulse responses (“IRs”) which can be used with Roomsim[2] to generate the corresponding room configuration and the multi-microphone audio tracks used in our research. In the “Text_setups” folder, one can find the Roomsim text setups for the microphones: C,HRN,L,R,V1,V2,VL,WW_L,WW_R,TR. The “IRs” folder contains two subfolders: “conf1” can be used to generate the recordings for the Mozart piece, and “conf2” for the Bruckner, Beethoven, and Mahler pieces. We provide IR “.mat” files for each of the pairs (“microphone”,”source”): microphone_Ssourcenumber.mat, where “microphone” is C,HRN,L,R,V1,V2,VL,WW_L,WW_R,TR, and “sourcenumber” is the number of the sources ordered as in this list: bassoon (1), cello(2), clarinet(3), double bass(4), flute(5), horn(6), viola(7), violin(8), oboe(9), trumpet(10). Please consider that the Mozart piece does not contain oboe nor trumpet.     Conditions of Use The annotations and the Roomsim configuration files in the PHENICX-Anechoic dataset are offered free of charge for non-commercial use only. You can not redistribute them nor modify them. Dataset by Marius Miron, Julio Carabias-Orti, Juan Jose Bosch, Emilia Gómez and Jordi Janer, Music Technology Group - Universitat Pompeu Fabra (Barcelona). This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. For the intellectual rights and the distribution policy of the audio recordings in this dataset contact Aalto University, Jukka Pätynen and Tapio Lokki. For more information about the original anechoic recordings we refer to the web page and the associated publication [2].   Please Acknowledge PHENICX-Anechoic in Academic Research When the present dataset is used for academic research, we would highly appreciate if scientific publications of works partly based on the PHENICX-Anechoic dataset quote the following publications:   M. Miron, J. Carabias-Orti, J. J. Bosch, E. Gómez and J. Janer, "Score-informed source separation for multi-channel orchestral recordings", Journal of Electrical and Computer Engineering (2016)   Pätynen, J., Pulkki, V., and Lokki, T., "Anechoic recording system for symphony orchestra," Acta Acustica united with Acustica, vol. 94, nr. 6, pp. 856-865, November/December 2008.   Download Dataset available Go to our download page.   Feedback Problems, positive feedback, negative feedback, help to improve the annotations... it is all welcome! Send your feedback to: marius.miron@upf.edu AND mtg@upf.edu In case of a problem report please include as many details as possible.   References [1] M. Miron, J. Carabias-Orti, J. J. Bosch, E. Gómez and J. Janer, "Score-informed source separation for multi-channel orchestral recordings", Journal of Electrical and Computer Engineering (2016) [2] Pätynen, J., Pulkki, V., and Lokki, T., "Anechoic recording system for symphony orchestra," Acta Acustica united with Acustica, vol. 94, nr. 6, pp. 856-865, November/December 2008. [2] Campbell, D., K. Palomaki, and G. Brown. "A Matlab simulation of" shoebox" room acoustics for use in research and teaching." Computing and Information Systems 9.3 (2005): 48.

opencc-by-4.0Jul 2017View details →

Annotation table - Whole body transcriptomes of the tick Ixodes ricinus at different stage and feeding conditions

Annotation table for a de novo assembled transcriptome of Ixodes ricinus in different stages and conditions. Description of the fields of each column (Trinotate results, and additionnal statistics): 1. Contig_name:  name of the contig (Trinity assembly) 2. sprot_Top_BLASTX_hit: first hit of the blastx search against SwissProt (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/) 3. TrEMBL_Top_BLASTX_hit: first hit of the blastx search against Uniref90 (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/) 4. RNAMMER: identification of non-coding RNAs 5. prot_id: identifier of the predicted protein (TransDecoder) 6. prot_coords: coordinates (start, end and strand) of the predicted protein on the contig 7. sprot_Top_BLASTP_hit: first hit of the blastp search between the predicted protein and SwissProt (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/) 8. TrEMBL_Top_BLASTP_hit: first hit of the blastp search between the predicted protein and Uniref90 (https://data.broadinstitute.org/Trinity/Trinotate v2.0 RESOURCES/) 9. Pfam: result of the search against PfamA database 10. SignalP: prediction of a signal peptide with SignalP 11. TmHMM: prediction of a transmembrane domain with THMM 12. eggnog: eggNOG database of orthologous genes (v3.0) assignation 13. gene_ontology_blast: GO assignation based on blast results 14. gene_ontology_pfam: GO assignation based on pfam results 15. Contig_length: length of the contig in bp 16. Busco_Id: name of the BUSCO (v1) 17. Busco_status: status of the BUSCO (complete/fragmented/duplicated) 18-32: Kallisto read counts for the 15 libraries A, B, C: unfed nymphs (replicates 1, 2, 3) D, E, F:  partially fed nymphs (replicates 1, 2, 3) G, H, I: males (unfed) (replicates 1, 2, 3) J, K, L: unfed adult females (replicates 1, 2, 3) M, N, O:  partially fed adult females (replicates 1, 2, 3) 33. log2FoldChange_UnfedVsPartiallyFed:  log fold change in base 2 of expression (comparison between "unfed" -including males- and "fed" ticks) 34. pvalue_UnfedVsPartiallyFed: p-value of the comparison between "unfed" -including males- and "fed" ticks 35. log2FoldChange_MaleVsFemale: log fold change in base 2 of expression (comparison between "males" and "females") 36. pvalue_MaleVsFemale: p-value of the comparison between "males" and "females" 37. log2FoldChange_NymphsVsAdults: log fold change in base 2 of expression (comparison between "nymphs" and "adults" -males and females-) 38. pvalue_NymphsVsAdults: p-value of the comparison between "nymphs" and "adults" -males and females-)

opencc-by-4.0Apr 2024View details →

SemTab 24: Semantic Table Annotations Benchmark for LLM-based approaches

SuperSemtab24 is a dataset for tabular data to knowledge graph matching. The dataset is divided into training and validation sets. The dataset includes general-purpose tables and intentionally misspelled entities to evaluate the model's robustness. Participants must annotate the entity mentions in the validation set and submit their annotations (following a target file). The repository contains the full version of the dataset; the ground truth (GT) of the test set will be uploaded in the future.

opencc-by-4.0Sep 2022View details →

Training data for 'Long non-coding RNAs (lncRNAs) annotation with FEELnc' tutorial (Galaxy Training Material)

Data needed for the 'Long non-coding RNAs (lncRNAs) annotation with FEELnc' tutorial (Galaxy Training Material). The assembly was generated following the 'Genome assembly using PacBio data' tutorial. The annotation was generated following the 'Genome annotation with Funannotate ' tutorial. The bam file is RNASeq SRR8534859_1.fastq.gz and SRR8534859_2.fastq.gz mapping on the genome assembly.

294B in Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation

294B. Bolitoglossa orestes. La Bravera, way from Mérida to La Azulita, Mérida, near type locality of the synonym B. spongai. Photo: César Barrio-Amorós.

282 in Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation

282. Pristimantis yuruaniensis. Female. Summit of Yuruani-tepui, Bolívar. Photo: César Barrio-Amorós.

279D in Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation

279D. Pristimantis vanadisae. Juvenile, spotted pattern. Estancia La Bravera, way from Mérida to La Azulita, 2,200 m asl, Mérida. Photo: César Barrio-Amorós.

279C in Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation

279C. Pristimantis vanadisae. Female, pattern dorsoconcolor. Estancia La Bravera, way from Mérida to La Azulita, 2,200 m asl, Mérida. Photo: César Barrio-Amorós.

279A in Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation

279A. Pristimantis vanadisae. Female, pattern plain. Estancia La Bravera, way from Mérida to La Azulita, 2,200 m asl, Mérida. Photo: César Barrio-Amorós.

275. Pristimantis sarisarinama. Paratopotype EBRG 4674 in Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation

275. Pristimantis sarisarinama. Paratopotype EBRG 4674. Sima Mayor Sarisariñama-tepui, Bolívar. Photo: César Barrio-Amorós.

272A. Pristimantis rivasi. Female holotype MHNLS 18445 in Catalogue of the amphibians of Venezuela: Illustrated and annotated species list, distribution, and conservation

272A. Pristimantis rivasi. Female holotype MHNLS 18445. Cerro Las Antenas, Sierra de Perijá, Zulia. Photo: Tito Barros.