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* 1. What is your job?

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* 2. What is the primary organism you work on?

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* 3. What type of work do you do? Check all that apply.

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* 4. What types of data do you create currently or expect to create within the next few years? Check all that apply.

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* 5. How often do you use CGD?

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* 6. From your perspective, what is the most important function of CGD? Please, drag and drop responses in order of importance, where 1 is the most important.

  1. Serving as a source of sequences for comparative genomics
  2. Providing access to data from high throughput experiments
  3. Curating of gene-specific information from literature
  4. Keeping the genome sequence and annotation up-to-date
  5. Access to Colleague information
  6. Access to Community news, meeting announcements, etc
  7. Linking references and genes specific to Candida-caused diseases
  8. Using the study of a given Candida species to inform the other species

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* 7. Is there any important function missing from Question 6? Please specify:

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* 8. CGD’s web pages were designed 25 years ago. How important is it to you to that the look and feel of CGD be modernized? For examples, see SGD and Pombase.

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* 9. What other resources do you use to help you in your research?

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* 10. Do these other resources fully serve your needs for your Candida research?

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* 11. What improvements to the CGD User Interface would you like to suggest? Please elaborate:

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* 12. Are there any search features not currently available at CGD that would be useful to you? Please elaborate:

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* 13. Please rate the following types of data with respect to their importance for incorporation into CGD, where 1 is most important/highest priority. Drag and drop answers in order of importance.

  1. Addition of Candida tropicalis to CGD
  2. Clustered expression data in an easily viewable format, e.g. GeneExplorer
  3. Gene expression data linked between genes and datasets
  4. Genetic Interaction data
  5. More prominent GO Slim sets
  6. Phenotype and GO data linked to the source reference
  7. Post-translational protein modification data, e.g. acetylation, phosphorylation, sumoylation
  8. Protein interaction data
  9. Searchable and/or sortable phenotype data
  10. Visualized protein complex data

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* 14. If RNA-seq data were converted to heat maps, such as this, would you find this format:

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* 15. Please rate the following aspects of manual literature-based curation with respect to their importance, where 1 is most important/highest priority. Drag and drop answers in order of importance.

  1. Gene Ontology curation
  2. Protein Interaction curation
  3. Collecting Mutant Phenotype data
  4. Gene-to-disease annotation

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* 16. Are there additional types of manually curated data that you would like to see included in CGD? Please elaborate:

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* 17. In addition to the Candida species currently curated at CGD (albicans, glabrata, dublinensis, parapsilosis, auris), which additional species would you choose as highest priority for us to incorporate and curate next?

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* 18. Do you use the JBrowse Genome Browser (see example)

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* 19. If so, what is the primary purpose for you to use JBrowse?

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* 20. Do you have other suggestions for new features or data to include in the JBrowse Genome Browser?

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* 21. Do you use the Homology Information pages in CGD (see example)?

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* 22. Do you have suggestions for new tools or data to improve access to the homology data?

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* 23. We use high-throughput sequence data to improve the genome sequences and their annotation in several ways.   Please rate the following with respect to their importance and priority to you, where 1 is most important/highest priority. Drag and drop answers in order of importance.

  1. Annotate upstream ORFs (uORFs) in 5’ UTRs
  2. Identify and display cases of alternative splicing
  3. Annotate novel transcripts, including antisense and non-coding
  4. Identify and display potential regulatory sequences (e.g. transcription factor binding sites)
  5. Identify and correct errors in the reference sequences

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* 24. Among the data types and analysis tools, please rate with respect to their importance and priority, where 1 is most important/highest priority. Drag and drop answers in order of importance.

  1. Expand the large-scale data types stored in CGD to include ChIP-Seq, ChIP-chip, proteomics and interactome data
  2. Incorporate multiple additional Candida genome sequences and phenotype data for sequenced strains
  3. Identify and display differences in gene structure of orthologs and paralogs, for example to identify cases of intron gain and loss

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* 25. Are there additional new data types or analysis tools that you would like us to incorporate? If so, please describe

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* 26. Do you have any other comments or suggestions for CGD?

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