Re: New tags for biology and medicine.
On 9/6/07, Benjamin Mesing [EMAIL PROTECTED] wrote: Hello, Are there packages out there, which work on general seqences (i.e. are independent of the type of the sequence). The utility sort comes to my mind, wich can work on many different types (numbers, strings, dates) What you describe is obviously a nice idea, but I think beyond the scope of debtags. A package for DNA analysis will probably not work when feeded with written language (without modification). And debtags is about describing what a package can do as it is. The complearn-tools package is one example; it works well with genetic sequences, protein sequences, written human languages, compiled executable code, and many other domains. It is in the class of algorithms called universal learners which have recently gained popularity. [1,2] This terminology is not without support given recent results in universal type theory. [3] Best regards, Rudi [1]: http://citeseer.ist.psu.edu/689388.html [2]: R. Cilibrasi, P.M.B. Vitanyi, Clustering by compression, IEEE Trans. Information Theory, 51:4(2005) [3]: Seroussi, Gadiel, On universal types, HPL-2004-153 20040917, HP Tech report +Tag: works-with::sequence:nuceleic +Description: Nucleic acids + Sequence of nucleic acids: DNA, RNA but also non-natural nucleic acids such as PNA or LNA. + +Tag: works-with::sequence:peptidic +Description: Proteins + Sequence of aminoacids: peptides and proteins. Quite detailed, though otherwise, people proably won't pick works-with::sequence if searching for algorithms working on a DNA. I made this proposition with the goal of having a lot of debian-med packages which manipulate sequence. In that context, the biologist would naturally want to distinguish between proteins and nucleic acids: this is a very common distinction. But shall we wait before we have, say 50 packages wihich have field::biology and works-with::sequence? I have suggested to move those into the biology:: facet, so you get full expressivity without bloating the works-with:: facet. +Tag: works-with-format::plaintext:aln +Tag: works-with-format::plaintext:fasta +Tag: works-with-format::plaintext:nexus This is definitely an area where there is an overlap between mime types and tags. But I would definitely be excited if debtags could propose toolchains which are connected by the formats they accept. Once again, we do not have the critical mass yet... Same here, I proposed to put them into biology::. A few words of the proposals you made in another mail: * ::bioinformatics, ::molecular-biology, ::structural-biology I would rather see field::biology:molecular than field::biology:molecular-biology, Sure. However, my proposal was to have biology::molecular-biology. Though, you seem to prefer to keep this in the main field facet, which is also ok. biology::molecular-biology:structural instead of biology::structural(-biology) may horrify some of our colleagues, though. I think you have misread my proposal here. Or I am misunderstand you. What would horrify your colleagues? * ::emboss I strongly advocate suite::emboss we will get the critical mass for it. Again I would move that into a biology facet. In conclusion, about the possiblity to manage ourselves our sets of tags. In the everyday work, one has a very narrow point of view of his tools. I use a PCR machine to make a PCR, I use a Pipetmanⓡ to pipette,... this could be expressed by biology::PCR, and biology::pipetting. But if we think harder, we can have a higher point of view. Instead of biology::PCR it would be use::amplification, or use::diagnostic, for instance, because the PCR machine produces DNA, but sometimes we want to keep it as a reagent, and some other times we just want to see its size and then we throw it away. So the questions I am wondering about are : - What is the most powerful approach ? - What is the expectations of our users ? - How can we interest our users in an unexpeced and powerful usage of the DebTags ? We had the dicussion of the degree of detail for the vocabulary (which is the set of facets and tags) before, and most agree that a high degree is desirable. The complexity of a larger number of tags can be made manageable by a good user interface. However, I think this applies only for the general purpose domain (i.e. search criteria required by the majority of users). The other special purpose domains like (devel, security, medicine,..) IMO should be provided in seperate modules of encapsulation (if you forgive me using this term from the software enginnering terminology) - which in this case can be represented as seperate facets. Within those facets a high degree of detail can be achieved again. I think that an advanced usage of Debtags is the only way to bring attention of users and ourselves to programs which we do not expect to be relevant to
Re: New tags for biology and medicine.
On Wed, 5 Sep 2007, Benjamin Mesing wrote: We had a short discussion on IRC about your proposal, and as far as we are concerned, Option 2. would be Ok for us (obviously Option 1. would also be ok, since we wouldn't have anything to do with that ;-). We would like to put the following tags in the main hierarchy either way: * field::medicine * use::comparison (though Enrico warned about the name - we would imagine a diff tool from that, but I think it is just fine to use it with different interpretation) * use::analysis * field::medicine:imaging (I wouldn't want to place that into biology:: and don't see the need for a med:: facet yet) I'm perfectly fine with this except the last item. The currently available packages for medical imaging do definitely not belong into a biology section. It is clearly about medicine and handles medical image formats like DICOM. Moreover we have a medical practice management system (GNUmed) which does not really fit in any yet existing category. If there are no objections I will add those in roughly a week. This would be great. And the following tags in the biology facet (note that I have adapted some of the tag names): * ::bioinformatics, ::molecular-biology, ::structural-biology (though those could go into field::biology if you rather see that) * ::format:aln, ::format:fasta, ::format:nexus (or would you rather have aln-format, fasta-format,..?) * ::emboss * ::nucleic-acids, ::peptides * ::alignment-analysis, ::phylogeny-analysis (if you really think this is neccessary) Once this is agreed upon and the remaining questions are answered, I will add the biology facet. I would regard this as a very reasonable compromise. We are not sure about the ::algorithm:* thing. They are not biology specific so it would be odd to put them there. Besides, Enrico pointed out, that nearly everything (at least the software) is made-of algorithms. Additionally, to me the whole made-of facet does not seem very concise anyways... I trust in Enricos sane experience. ;-)) Kind regards Andreas. -- http://fam-tille.de ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
On Thu, 2007-09-06 at 09:11 +0200, Andreas Tille wrote: On Wed, 5 Sep 2007, Benjamin Mesing wrote: We had a short discussion on IRC about your proposal, and as far as we are concerned, Option 2. would be Ok for us (obviously Option 1. would also be ok, since we wouldn't have anything to do with that ;-). We would like to put the following tags in the main hierarchy either way: * field::medicine * use::comparison (though Enrico warned about the name - we would imagine a diff tool from that, but I think it is just fine to use it with different interpretation) * use::analysis * field::medicine:imaging (I wouldn't want to place that into biology:: and don't see the need for a med:: facet yet) I'm perfectly fine with this except the last item. The currently available packages for medical imaging do definitely not belong into a biology section. It is clearly about medicine and handles medical image formats like DICOM. Moreover we have a medical practice management system (GNUmed) which does not really fit in any yet existing category. I think you have misunderstood me. It's the same that I thought. Therefore I left it in the field:: facet as field::medicine:imaging. Regards Ben ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
Dear all, I was a bit lazily waiting for the conversation to settle before trying to aswer :) +Tag: field::biology:bioinformatics +Tag: field::biology:molecular +Tag: field::biology:structural This is probably a reasonable distinction, though we have to decide if we want such a fine-grained separation of the field facet. We would also end up with needing the same level of detail for electronics, chemistry, physics,... I think that I would have a pragmatic approach : fine-graining as long as there is a consensual demand. By this I mean that fine-graing a facet should not become a hassle for the package maintainers who are not interested in them. In the case of the Debian-Med project, I think that each time we will propose such kind of tags it will mean that we have people dedicated to screen all the parent tags and assign the fine-grained if necessary. (by the way, could there be a subscription mechanism to monitor addition and removal of tags ?) +Tag: field::medicine:imaging I support creating field::medicine:imaging, and using field::biology + use::analysis and works-with::image instead of field::biology:imaging. I think that as long as we do not package software such as microscope control tools it would make sense. field::medicine:imaging, on the other hand, already have candidate package whose usage is broader than just taking and viewing pictures. +Tag: made-of::algorithm:dynamic-programming +Tag: made-of::algorithm:hashing +Tag: made-of::algorithm:hidden-markov-model +Tag: made-of::algorithm:neural-network I like the idea, but I see that it is not consensual, and I think that we did not reach a critical mass yet. I propose to postpone: let us keep the proposition in debian-med's SVN, and see in a few monthes when we have improved our coverage. +Tag: works-with::sequence +Description: Sequence + The program manipulates data made of a sequence of elements from a finite set. Somehow this is different to the current tags in works-with, but I believe it could fit in. E.g. sorting applications could also fit in here? I think that this is exactly the goal. Sometimes there is innovative research which is done by taking tools for analysing genome sequence and utilizing them on written language, or vice-versa. I would see this tag with a high level of abstraction. +Tag: works-with::sequence:nuceleic +Description: Nucleic acids + Sequence of nucleic acids: DNA, RNA but also non-natural nucleic acids such as PNA or LNA. + +Tag: works-with::sequence:peptidic +Description: Proteins + Sequence of aminoacids: peptides and proteins. Quite detailed, though otherwise, people proably won't pick works-with::sequence if searching for algorithms working on a DNA. I made this proposition with the goal of having a lot of debian-med packages which manipulate sequence. In that context, the biologist would naturally want to distinguish between proteins and nucleic acids: this is a very common distinction. But shall we wait before we have, say 50 packages wihich have field::biology and works-with::sequence? +Tag: works-with-format::plaintext:aln +Tag: works-with-format::plaintext:fasta +Tag: works-with-format::plaintext:nexus This is definitely an area where there is an overlap between mime types and tags. But I would definitely be excited if debtags could propose toolchains which are connected by the formats they accept. Once again, we do not have the critical mass yet... I am not sure it is a good idea to put those beneath plaintext. There are the two cases: 1. Someone searching for a tool for editing plaintext would end up with the special purpose plaintext:aln editors, which IMO is undesirable. 2. Someone searching for a special purpose plaintext:aln editor could deduce from the tag name, that he could also use plaintext, and if he knows that ALN is a plaintext format he could navigate there smoothly (which assumes that the tags are displayed in a hierarchical manner). So the formats could as well be top level. Though this would mean cluttering the works-with-format facet. Could there be a works-with-format::special-purpose:* group? Do we need a way to express releationships beween tags like: show works-with-format::plaintext:aln only if field::biology or field::medicine is selected? Or do we want to cover this by requiring sophisticated UIs, which detect this in an automatic fashion. I will bravely let you choose, as you know much better Debtags than I do. I think that it could be useful to know that fasta, nexus, aln, ... are plaintext format. +Tag: use::comparison:alignment +Description: Alignment + To identify similarities in two objects by maximising the overlap of identical parts. + +Tag: use::comparison:phylogeny +Description: Phylogenetic analysis + To infer lineage relationships. Those seems to be covered by use analysis to me. Alignment and phylogeny are very
Re: New tags for biology and medicine.
Hello, On Thu, 2007-09-06 at 20:30 +0900, Charles Plessy wrote: Dear all, I was a bit lazily waiting for the conversation to settle before trying to aswer :) +Tag: field::biology:bioinformatics +Tag: field::biology:molecular +Tag: field::biology:structural This is probably a reasonable distinction, though we have to decide if we want such a fine-grained separation of the field facet. We would also end up with needing the same level of detail for electronics, chemistry, physics,... I think that I would have a pragmatic approach : fine-graining as long as there is a consensual demand. By this I mean that fine-graing a facet should not become a hassle for the package maintainers who are not interested in them. In the case of the Debian-Med project, I think that each time we will propose such kind of tags it will mean that we have people dedicated to screen all the parent tags and assign the fine-grained if necessary. There are two more things to consider: 1. the users who do searching based on tags and 2. the people doing the tagging. With each tag, the complexity of the vocabulary will be increased and only a small percentage of the people mentioned above is interested in the level of detail provided by the med-specific tags. However, they have to deal with those tags either way. To reduce the burden of those people it is, that I proposed to keep the tags in a separate facet. It might even make things easier for med-interested people, because they would probably recognise the biology:: facet as an important one and go straight there to look for interesting tags. (by the way, could there be a subscription mechanism to monitor addition and removal of tags ?) I believe the best thing right now is an SVN diff, which could theoretically be hooked into sending an email upon changes. However, no such thing is currently implemented (I believe). +Tag: works-with::sequence +Description: Sequence + The program manipulates data made of a sequence of elements from a finite set. Somehow this is different to the current tags in works-with, but I believe it could fit in. E.g. sorting applications could also fit in here? I think that this is exactly the goal. Sometimes there is innovative research which is done by taking tools for analysing genome sequence and utilizing them on written language, or vice-versa. I would see this tag with a high level of abstraction. Are there packages out there, which work on general seqences (i.e. are independent of the type of the sequence). The utility sort comes to my mind, wich can work on many different types (numbers, strings, dates) What you describe is obviously a nice idea, but I think beyond the scope of debtags. A package for DNA analysis will probably not work when feeded with written language (without modification). And debtags is about describing what a package can do as it is. +Tag: works-with::sequence:nuceleic +Description: Nucleic acids + Sequence of nucleic acids: DNA, RNA but also non-natural nucleic acids such as PNA or LNA. + +Tag: works-with::sequence:peptidic +Description: Proteins + Sequence of aminoacids: peptides and proteins. Quite detailed, though otherwise, people proably won't pick works-with::sequence if searching for algorithms working on a DNA. I made this proposition with the goal of having a lot of debian-med packages which manipulate sequence. In that context, the biologist would naturally want to distinguish between proteins and nucleic acids: this is a very common distinction. But shall we wait before we have, say 50 packages wihich have field::biology and works-with::sequence? I have suggested to move those into the biology:: facet, so you get full expressivity without bloating the works-with:: facet. +Tag: works-with-format::plaintext:aln +Tag: works-with-format::plaintext:fasta +Tag: works-with-format::plaintext:nexus This is definitely an area where there is an overlap between mime types and tags. But I would definitely be excited if debtags could propose toolchains which are connected by the formats they accept. Once again, we do not have the critical mass yet... Same here, I proposed to put them into biology::. A few words of the proposals you made in another mail: * ::bioinformatics, ::molecular-biology, ::structural-biology I would rather see field::biology:molecular than field::biology:molecular-biology, Sure. However, my proposal was to have biology::molecular-biology. Though, you seem to prefer to keep this in the main field facet, which is also ok. biology::molecular-biology:structural instead of biology::structural(-biology) may horrify some of our colleagues, though. I think you have misread my proposal here. Or I am misunderstand you. What would horrify your colleagues? * ::emboss I strongly advocate suite::emboss we will get the critical mass for it. Again I would move that into a
Re: New tags for biology and medicine.
Le Thu, Sep 06, 2007 at 10:21:57PM +0200, Benjamin Mesing a écrit : There are two more things to consider: 1. the users who do searching based on tags and 2. the people doing the tagging. With each tag, the complexity of the vocabulary will be increased and only a small percentage of the people mentioned above is interested in the level of detail provided by the med-specific tags. Hello, nobody wants to be lost in a space with too many dimentions which are almost empty. This is why I would prefer to express the properties of the package with already existing tags rather than with private biology:: tags. But I will of course not oppose anybody using this approach, and will do my best so that the packages in our radar are using them appropriately if they exist. So unless there is a new idea popping out, my recommendation is to commit the tags for which we all aggreed on, and re-open the discussion in a few monthes where: - we in Debian-Med have extended our software coverage, - you have got diverse feedback from other Debian teams. Have a nice day, PS: biology::molecular-biology:structural instead of biology::structural(-biology) may horrify some of our colleagues, though. I think you have misread my proposal here. Or I am misunderstand you. What would horrify your colleagues? That structural biology is a whole discipline of its own, and not a mere offspring of molecular biology ;) -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
Hello Thus we need to decide, if those details should become part of the main vocabulary database. Well, I don't think that we should make a harsh difference compared to the main vocabulary database. Considering the effect of a less fine grained tagging: People will be presented a list of (guess) 20 items instead of 3-5 items for the more fine grained list, but I think 20 packages in a list are manageable. The danger of bloating the system with about 15 more packages you might not need is not really a thing many people are scary about. Sorry, I can't really follow your thoughts here, do you vote against a fine-grained tagging? With the fine-grained tags, you will have more tags, but usually a smaller result set (i.e. package list). So what you are bloating is the vocabulary (the set of all available tags and facets). Another way would be to provide them in a different vocabulary/tag database - debtags supports multiple of those. Just for the sake of academical interest: What are the consequences of a differnet vocabulary/tag database? I guess the drawback is higher than a fine grained tagging. Advantages: * clean separation * you keep the full expressivity of the main vocabulary (i.e. you can add tags into the other facets like works-with, made-of...) Disadvantages: * additional administrative overhead for hosting the tag database * additional overhead for users of this tag database, which must be enabled one way or another * tagging infrastructure must be provided (or happen centrally by the Debian-med team) +Tag: field::biology:bioinformatics +Description: Bioinformatics + Sequence analysis software. + +Tag: field::biology:molecular +Description: Molecular biology + Software useful to molecular cloning and related wet biology. + +Tag: field::biology:structural +Description: Structural biology + Software useful to model tridimentional structures. + This is probably a reasonable distinction, though we have to decide if we want such a fine-grained separation of the field facet. I also wonder whether we gain much at users and. It might happen that users have a slightly different perception of these terms and we could This would hint to have them only inside a special debian-med:: area. We would also end up with needing the same level of detail for electronics, chemistry, physics,... Well, this is always the same - you need someone who does the job. Debian-Med just joins forces for people interested in medicine and biology so we are a little bit ahead. :) Sure, I am not saying that we actually *need* the level of detail there, but that eventually the same level of detail will arise in the other areas, which will bloat the vocabulary. Regards Ben ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
Hello, I believe it is past time to react to this proposal, we don't want to be seen as some kind of black hole, everything that goes in never comes out. And since I have some spare time at hand, I will make a start. Generally speaking the proposed tags are relativly detailed. I believe this level of detail is required only by biologists or people in the medical field. Thus we need to decide, if those details should become part of the main vocabulary database. Another way would be to provide them in a different vocabulary/tag database - debtags supports multiple of those. Below you can find my thoughts towards the proposal under the assumption that the tags should become part of the main database. Index: debian-packages === --- debian-packages (révision 2253) +++ debian-packages (copie de travail) @@ -559,6 +559,18 @@ +Tag: field::biology:bioinformatics +Description: Bioinformatics + Sequence analysis software. + +Tag: field::biology:molecular +Description: Molecular biology + Software useful to molecular cloning and related wet biology. + +Tag: field::biology:structural +Description: Structural biology + Software useful to model tridimentional structures. + This is probably a reasonable distinction, though we have to decide if we want such a fine-grained separation of the field facet. We would also end up with needing the same level of detail for electronics, chemistry, physics,... +Tag: field::medicine +Description: Medicine I believe that one is agreed upon. +Tag: field::medicine:imaging +Description: Medical Imaging + Same as for the ::biology:* tags +Tag: made-of::algorithm:dynamic-programming +Description: Dynamic programming + +Tag: made-of::algorithm:hashing +Description: Hashing + +Tag: made-of::algorithm:hidden-markov-model +Description: Hiden Markov Model (HMM) + +Tag: made-of::algorithm:neural-network +Description: Neural Network + Can you please give an example of such a package? I have no idea how a package made of an algorithm looks like. +Tag: works-with::sequence +Description: Sequence + The program manipulates data made of a sequence of elements from a finite set. Somehow this is different to the current tags in works-with, but I believe it could fit in. E.g. sorting applications could also fit in here? +Tag: works-with::sequence:nuceleic +Description: Nucleic acids + Sequence of nucleic acids: DNA, RNA but also non-natural nucleic acids such as PNA or LNA. + +Tag: works-with::sequence:peptidic +Description: Proteins + Sequence of aminoacids: peptides and proteins. Quite detailed, though otherwise, people proably won't pick works-with::sequence if searching for algorithms working on a DNA. +Tag: works-with-format::plaintext:aln +Description: Clustal/ALN + Used in multiple alignment of biological sequences. + +Tag: works-with-format::plaintext:fasta +Description: Fasta/Pearson + Very popular format for biological sequencs. + +Tag: works-with-format::plaintext:nexus +Description: Nexus + Popular format for phylogenetic trees. I am not sure it is a good idea to put those beneath plaintext. There are the two cases: 1. Someone searching for a tool for editing plaintext would end up with the special purpose plaintext:aln editors, which IMO is undesirable. 2. Someone searching for a special purpose plaintext:aln editor could deduce from the tag name, that he could also use plaintext, and if he knows that ALN is a plaintext format he could navigate there smoothly (which assumes that the tags are displayed in a hierarchical manner). So the formats could as well be top level. Though this would mean cluttering the works-with-format facet. Could there be a works-with-format::special-purpose:* group? Do we need a way to express releationships beween tags like: show works-with-format::plaintext:aln only if field::biology or field::medicine is selected? Or do we want to cover this by requiring sophisticated UIs, which detect this in an automatic fashion. +Tag: suite::emboss +Description: EMBOSS + Software and data related to the European Molecular Biology Open Software Suite. + Sounds good to me. +Tag: use::analysis +Description: Analysis + Software for turning data into knowledge. + Agreed. +Tag: use::comparison +Description: Comparison + To find what relates or differs in two or more objects. Agreed. + +Tag: use::comparison:alignment +Description: Alignment + To identify similarities in two objects by maximising the overlap of identical parts. + +Tag: use::comparison:phylogeny +Description: Phylogenetic analysis + To infer lineage relationships. Those seems to be covered by use analysis to me. Thanks Charles for brining the topic up again. Regards Ben ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
On Tue, 4 Sep 2007, Benjamin Mesing wrote: I believe it is past time to react to this proposal, we don't want to be seen as some kind of black hole, everything that goes in never comes out. And since I have some spare time at hand, I will make a start. Generally speaking the proposed tags are relativly detailed. I believe this level of detail is required only by biologists or people in the medical field. Probably. Thus we need to decide, if those details should become part of the main vocabulary database. Well, I don't think that we should make a harsh difference compared to the main vocabulary database. Considering the effect of a less fine grained tagging: People will be presented a list of (guess) 20 items instead of 3-5 items for the more fine grained list, but I think 20 packages in a list are manageable. The danger of bloating the system with about 15 more packages you might not need is not really a thing many people are scary about. Another way would be to provide them in a different vocabulary/tag database - debtags supports multiple of those. Just for the sake of academical interest: What are the consequences of a differnet vocabulary/tag database? I guess the drawback is higher than a fine grained tagging. Index: debian-packages === --- debian-packages (révision 2253) +++ debian-packages (copie de travail) @@ -559,6 +559,18 @@ +Tag: field::biology:bioinformatics +Description: Bioinformatics + Sequence analysis software. + +Tag: field::biology:molecular +Description: Molecular biology + Software useful to molecular cloning and related wet biology. + +Tag: field::biology:structural +Description: Structural biology + Software useful to model tridimentional structures. + This is probably a reasonable distinction, though we have to decide if we want such a fine-grained separation of the field facet. I also wonder whether we gain much at users and. It might happen that users have a slightly different perception of these terms and we could We would also end up with needing the same level of detail for electronics, chemistry, physics,... Well, this is always the same - you need someone who does the job. Debian-Med just joins forces for people interested in medicine and biology so we are a little bit ahead. :) +Tag: field::medicine +Description: Medicine I believe that one is agreed upon. +Tag: field::medicine:imaging +Description: Medical Imaging + Same as for the ::biology:* tags Well, I do not agree here completely. We have a fair amount of packages (becoming more soon) that deal with medical imaging. If people are interested just in imaging they probably do not like things like a practice management system (depending on PostgreSQL server and other stuff). So IMHO this differentation might be worth the effort, but if you think it would spoil the principle of keeping things simple - just leave it out. Quite detailed, though otherwise, people proably won't pick works-with::sequence if searching for algorithms working on a DNA. I'm afraid you are right here. So the formats could as well be top level. Though this would mean cluttering the works-with-format facet. Could there be a works-with-format::special-purpose:* group? Sounds very reasonable. Thanks for your input. It partly shows that outsiders are able to bring some abstraction into the focussed view of specialists. Kind regards Andreas. -- http://fam-tille.de ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
Hello, On Tuesday 04 September 2007 12:10:30 Benjamin Mesing wrote: Generally speaking the proposed tags are relativly detailed. I believe this level of detail is required only by biologists or people in the medical field. Thus we need to decide, if those details should become part of the main vocabulary database. Another way would be to provide them in a different vocabulary/tag database - debtags supports multiple of those. [...] +Tag: field::biology:structural +Description: Structural biology + Software useful to model tridimentional structures. + This is probably a reasonable distinction, though we have to decide if we want such a fine-grained separation of the field facet. We would also end up with needing the same level of detail for electronics, chemistry, physics,... Yes, I think we do. The following two reasons jump to mind: * When thinking about automated installations of software (i.e. in grid computing) we need a language that allows us to talk about what is eligible for installations and what is not. Debtags are not perfect and other efforts describing various kinds of properties that software can have, there is nothing as sweet as Debtags to talk about what the software is actually doing. * Debian integrates communities. This is my way to read Custom Debian Distributions that are basically saying they people flock together to extend Debian towards a particular direction. Specialisation of Debian comes with a specialisation of terms. It is natural. I like the above sketched suggestion to allow for disjunct sets of facets that are maintained by different communities. It would seem natural to me to eventually allow for sub-facets of some kind with a higher number of : in their IDs to thus allow for an easier reduction of complexity. Though ... well ... it may not be needed tomorrow. Many greetings Steffen signature.asc Description: This is a digitally signed message part. ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
Re: New tags for biology and medicine.
On Tue, 4 Sep 2007, Steffen Moeller wrote: * When thinking about automated installations of software (i.e. in grid computing) we need a language that allows us to talk about what is eligible for installations and what is not. Debtags are not perfect and other efforts describing various kinds of properties that software can have, there is nothing as sweet as Debtags to talk about what the software is actually doing. Well, I'm convinced that DebTags might be a very great tools for different things, but I doubt that it is the best idea to base installations of clusters on DebTags technology. You certainly want to know _exactly_ what is installed on your cluster and do not really want it to be changed by any change in the DebTags database. I think for this purpose the meta package approach is the better way to go. * Debian integrates communities. This is my way to read Custom Debian Distributions that are basically saying they people flock together to extend Debian towards a particular direction. Specialisation of Debian comes with a specialisation of terms. It is natural. Sure. But I think subsetting makes sense in case your main set is to large to be managed with the means you have at hand. IMHO this is actually not (yet) the case. We want to extend Debian but I don't think that we should try to make a science out of classifying and subsetting what finally might end up on a real live installation all together again. I like the above sketched suggestion to allow for disjunct sets of facets that are maintained by different communities. It would seem natural to me to eventually allow for sub-facets of some kind with a higher number of : in their IDs to thus allow for an easier reduction of complexity. Though ... well ... it may not be needed tomorrow. I think we could wait with our fine grained subsets until this is implemented. Once this is done also the number of packages that rectifies a more fine grained subsetting will have increased. :) Kind regards Andreas. -- http://fam-tille.de ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
New tags for biology and medicine.
Hi Debtags team ! This is the monthly reminder that the Debian-Med team proposed new tags in May, http://lists.alioth.debian.org/pipermail/debtags-devel/2007-May/001630.html http://lists.alioth.debian.org/pipermail/debtags-devel/2007-July/001658.html Have a nice day, -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan ___ Debtags-devel mailing list Debtags-devel@lists.alioth.debian.org http://lists.alioth.debian.org/mailman/listinfo/debtags-devel
