Appendix E: notes from semi-structured interviews, Group A2 GoPubMed/GoGene interviews ========================== GoPubMed/GoGene user 1 Job Title and Responsibilities: PhD student, Systems Biology Time in [organisation] and/or in the profession 8 years in Biology (of which 6 in Bioinformatics) What made you decide to do the evaluation? Friends (personal contact) What did you think? The evaluation was fast and easy, so the system. What would make you want to use the Sealife browser (GoGene/GoPubMed) regularly? Adding links to Ensembl would be nice. The “Advanced Search” feature should become more visible (to get full functionality of the tool). Further discussion: GoGene is very useful for functional annotations of genes, throwing in a set of genes and looking at the GO terms. GoPubMed/GoGene user 2 Job Title and Responsibilities: PhD student, Systems Biology Time in [organisation] and/or in the profession: 5 years in Biotechnology What made you decide to do the evaluation? Friends (personal contact) What did you think? There should be a clear time limit for the evaluation (timer?). What would make you want to use the Sealife browser (GoGene/GoPubMed) regularly? It was a bit overloaded, the input was too much to go through everything. The user is “used” to the simple PubMed interface. Perhaps the initial interface should be simpler and then gradually expand into the full results. Further discussion: Liked the GoGene “summary” and “details”. Would like to have links to Ensembl. GoPubMed/GoGene user 3 Job Title and Responsibilities: PhD Student What made you decide to do the evaluation? Previously used PubMed but it was “really horrible” to find anything so normally she tries to use only Google for searching for papers. What did you think? Easy to get an overview, and to find more information. What would make you want to use the Sealife browser regularly? Physicist, so most of the articles are not in this database, but for biological purposes she thinks she would use it. If there were a similar system for physicists she would probably use that. For her GoPubMed is really easy because if you have no idea about biology and you are searching for a special protein you get a better overview with not too many details. GoPubMed/GoGene user 4 Job Title and Responsibilities: Post-Doc (computational biology) Time with [organisation] and/or in the profession and/or area of study and time in this area: 2 years What made you decide to do the evaluation? Friend of [evaluator] What did you think? Somehow useful just to get an idea, get to know some genes, like an overview. But somehow, the tools are OK for some searches, but are bad for others. Navigation tree on left was very useful but still it needs to be improved. For Go terms, you get three different Go categories, but you have no ranking. Not sure if the terms that appear are the top ranking or not. When he asked it to find “conserved domain” couldn’t find it because he couldn’t find the molecular properties of the genes being analysed. Would help to give keywords of the domain being searched. Always used single gene name and also tried to put “conserved domain” the engine didn’t work. But it’s OK when you have to find the process or the function. Maybe it works better with the functions or the pathway. Not so easy to find structural information like domains/concept domains, etc. What would make you want to use the Sealife browser regularly? If those things were improved he might want to use the Go systems regularly. The traditional PubMed is not good, so uses it just for papers, but he uses it just out of habit and uses Google much more as it provides the same results, and even more. GoPubMed/GoGene user 5 Job Title and Responsibilities: PhD bioinformatics Time with [organisation] and/or in the profession and/or area of study and time in this area: 2 years What made you decide to do the evaluation? Friend of [evaluator], also has heard many talks about this as she works with [other evaluator]; it’s interesting to help out with the development of the tools What did you think? Really likes GoPubMed and the sorting tree, but is still not using it so often that she automatically remembers what the sorting categories are. Helpful, but still needs to learn how to use it more efficiently. And of course it’s much better than PubMed with 10,000 results and reading all the abstracts at random so, even if she’s not as efficient as she could be, it’s still much better. Habits carry over from PubMed in putting in the keywords of interest, but this sometimes doesn’t give any results. So it would be nice to have more examples of keywords you could use for the search. E.G. if your keyword is a go term, you could put (go) in brackets. And if you are looking for a known name (au) it sometimes doesn’t give results even though you know they’re there. She showed this to her biologist friends and they just typed things in simply and couldn’t retrieve any results because of their habits – but once you know it, you know it and it’s fine. Knowledge of the system is key. What would make you want to use the Sealife browser regularly? Would be nice to get a direct link to the journals from GoPubMed, so much clicking all the time. Maybe have a feature to get many papers at once (even though she thinks this is difficult/not realistic to ask for!) – several results clustered. Would like system to suggest related links. Further discussion: Just for the GoGene, it would be nice to know all the synonyms that you use for that one gene, so you could get related genes & also the gene that you were querying. Gene summary was really good. Would also like to see all the possible synonyms. So you have to consider all the namings for this gene. Really liked GoGene and this was the first time she really used it, especially the last feature where you can search the sequence. Will use GoGene from now on! GoPubMed/GoGene user 6 Job Title and Responsibilities: Post doc Time with [organisation] and/or in the profession: 2 months post doc 7 years in the profession, since started PhD What made you decide to do the evaluation? [evaluator] What did you think? Used GoPubmed before but liked GoGene more What would make you want to use the Sealife browser regularly? Would use PubMed, not GoPubmed (this could be only useful if I am not satisfied with PubMed results) Gogene – yes I would use, I found Blast very convenient – good if I do want to know about a gene very quickly and good for using complex queries Further discussion: Navigation tree is nice and good for complex queries But not customisable (I would suggest to customise GoGene by adding protein-to-protein interaction, modify scoring of results, clearly let user see and let influence the scoring by user provided references) – there should be a clickable, typing wizard to represent the customisation - export references in machine readable way (e.g. XML, Web API) - interface – nice but messy, the tree is ok as it is expandable, recommend to flash the work you searched for or highlight the word in some way - recommend to allow weighing terms - for example if searching for 10 works allow AND, OR, weighing - other application of the semantic browser: useful to classify your own publications Evaluation of the evaluation: Say openly that it would take 1 and a half hours, not 1 hour And questions should be separate for GoPubMed and GoGene GoPubMed/GoGene user 7 Job Title and Responsibilities: PhD student Time with the HPA and/or in the profession 1 and ˝ years What made you decide to do the evaluation? [evaluator] is my friend, ipod and lunch too What did you think? There is potential; interface is too crowded to find information What would make you want to use the Sealife browser regularly? yes Further discussion: I would make the interface less busy as now all information is presented simultaneously I would not use GoPubMed But like EntrezGene (sp?) – where I can click for further information if I am interested rather than being presented all in one go I believe I would be more successful searching if using EntrezGene directly He liked the interface, it was pleasing to the eye and there was too much stuff Navigation was not clear, too confusing The tree on the left was clear but I prefer finding information in a linear step-by-step way – this was too much Can’t visualise the [semantic browser] outside gene context as I can’t see how else to apply it [SB] Liked the interface provided by UCSC Genome browser – providing you with options – I want X or – I don’t want X etc (repeated he liked a linear navigation style) GoPubMed/GoGene user 8 Job Title and Responsibilities: Bioinformatics Assistant Time with [organisation] and/or in the profession: 6 yrs What made you decide to do the evaluation? Interest in Ontology What did you think? I liked it What would make you want to use the Sealife browser regularly? Integration of more data resources GoPubMed/GoGene user 9 Job Title and Responsibilities: Bioinformatics Postdoc Time with [organisation] and/or in the profession: 5 yrs What made you decide to do the evaluation? Pressure from above What did you think? Quite useful What would make you want to use the Sealife browser regularly? More user-friendliness, non-obvious links, too much detail on the pages Further discussion: GoGene: from look and feel, it should be more like Gene page at NCBI GoPubMed/GoGene user 10 Job Title and Responsibilities: Graduate Student Genetics Time with [organisation] and/or in the profession: 1 yrs What made you decide to do the evaluation? Interest in GoGene What did you think? More practice is needed What would make you want to use the Sealife browser regularly? more time to explore the system Further discussion: Suggestions: hide parts of tree, if not useful to me and retain same tree for future usage GoPubMed/GoGene user 11 What made you decide to do the evaluation? Explore new tools What did you think? Really useful What would make you want to use the Sealife browser regularly? Quite powerful, no new additions needed for my usage Further discussion: I need more time to explore the system to provide points of discussion. GoPubMed/GoGene user 12 Job Title and Responsibilities: PhD Student What made you decide to do the evaluation? explore GoPubMed/GoGene What did you think? 2 really useful tools What would make you want to use the Sealife browser regularly? More user friendliness, more obvious links Further discussion: Problems with GoPubMed: difficulty answering question, maybe missed links