16:26:32 <RRSAgent> RRSAgent has joined #hcls
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16:26:40 <ericP> meeting: HCLS
16:26:45 <ericP> meeting: HCLS F2F
16:27:00 <ericP> chair: Scott Marshall
16:27:06 <ericP> scribenic: ericP
16:27:25 <Zakim> -Yong
16:27:45 <ericP> leina: U Texas
16:28:00 <ericP> ... pushing experimental data into SemWeb
16:28:25 <ericP> Don Doherty: neurscientist
16:28:35 <ericP> ... started company "BrainStage"
16:29:01 <ericP> Kei: faculty at Yale Center for BioInformatics
16:29:22 <ericP> ... working on SemWeb for integrating Neuroscience info
16:29:27 <ericP> ... member of SenseLab
16:30:49 <ericP> Alan Hobbs: neuroscientist at Kaieser Permanente
16:30:49 <ericP> ... collegue Peter Hendler will be here tomorrow to present SNOMED/OWL
16:31:04 <ericP> Masao: am Keio site manager
16:31:38 <ericP> ... today mostly working on home networks (not connected to SemWeb), but need to bring HCLS message back to Japan
16:31:57 <ericP> Harold Solbrieg: description logics with NCBO
16:32:17 <ericP> ... creating services for access to terminilogical content
16:32:41 <ericP> Micheal Miller: involved with Microarray gene expression standards
16:32:49 <ericP> ... importing data into rosetta net
16:33:38 <ericP> Fahim: neuoroscience information framework at UC San Diego
16:33:52 <ericP> Johsua Phillips: working on CaBig
16:34:03 <ericP> ... exposing linked data to CaBig
16:34:22 <ericP> ... using ontologies to connect data
16:35:13 <ericP> Susie: cochair of HCLS group
16:35:27 <ericP> ... working on LODD and TMO
16:35:41 <ericP> ... do participate on others, like SciDisc
16:35:51 <ericP> ... am director of science and tech at J&J
16:36:06 <mscottm> remote participants, please use the LiveMeeting link for *Monday* at the bottom of http://esw.w3.org/topic/HCLSIG/Meetings/2009-11-02_F2F
16:36:11 <mscottm> Zakim, who is here?
16:36:11 <Zakim> On the phone I see +1.610.651.aaaa, +1.408.988.aabb, matthias_samwald
16:36:12 <Zakim> On IRC I see RRSAgent, mscottm, Zakim, matthias_samwald, Cloud, ericP
16:36:15 <ericP> matthias_samwald: started out in neuroscience, specialized in semweb and ontologies
16:36:25 <ericP> ... working at DERI Gallway
16:36:42 <ericP> ... involved in lots of SemWeb cognitive projects
16:36:59 <ericP> ... creating standards and conventions which can be adopted on a wide scale
16:37:04 <ericP> Zakim, who is here?
16:37:04 <Zakim> On the phone I see +1.610.651.aaaa, +1.408.988.aabb, matthias_samwald
16:37:05 <Zakim> On IRC I see RRSAgent, mscottm, Zakim, matthias_samwald, Cloud, ericP
16:37:32 <ericP> Zakim, aaaa is Susie
16:37:32 <Zakim> +Susie; got it
16:37:43 <ericP> Zakim, aabb is HCLSf2f
16:37:43 <Zakim> +HCLSf2f; got it
16:38:50 <ericP> Nigam Shah: Stanford U NCBO
16:39:06 <ericP> Jeff: San Diego ...
16:39:22 <ericP> Micheal: @@@
16:39:34 <ericP> ... Roche pharmaceuticals
16:42:40 <LenaDeus> LenaDeus has joined #hcls
16:43:17 <masao> masao has joined #hcls
16:43:19 <solbrig> solbrig has joined #hcls
16:44:16 <Allen> Allen has joined #hcls
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16:44:34 <matthias_samwald> is there a link for the presentation?
16:44:47 <nigam> nigam has joined #hcls
16:44:51 <matthias_samwald> http://esw.w3.org/topic/HCLSIG/Meetings/2009-11-02_F2F?action=AttachFile&do=get&target=DonaldDohertyHCLS2009.pdf
16:44:53 <matthias_samwald> see it now
16:45:13 <ericP> topic: Overview of neuroscience and informatics requirements [Don Doherty]
16:46:46 <ericP> Don: spend a year busy with buisiness stuff
16:47:07 <ericP> ... you got a lot from Maryanne Martone (running NIF) last year 
16:48:05 <ericP> ... informatics underrepresented at recent neuro conference
16:48:24 <ericP> [slide 2] [picture of brain]
16:48:50 <ericP> ... most complex piece of matter, examined for 2K years
16:49:09 <ericP> [slide 3] Nicolaus Steno
16:49:54 <ericP> ... "to learn a machine, either the master who made it must show us it's artifice, or we have to take it apart and examine it"
16:50:07 <ericP> [slide 4]
16:51:09 <mscottm> Don: .. once Watson and Crick figured out the structure of DNA that lead to a lot of new developments
16:51:16 <Susie> Susie has joined #hcls
16:51:28 <mscottm> Don: .. Linus Pauling figured out the structural chemistry of Vita C
16:51:31 <ericP> Don: haven't had the "double-helix revelation" for the brain
16:51:41 <ericP> ... we can do microarrays in the brain
16:51:57 <ericP> [slide 5] Frueud's project
16:52:18 <ericP> Don: Freud started as an anatomist
16:52:40 <ericP> ... scientists needed independent support, so became a doctor
16:53:02 <ericP> ... wrote up a book on cognitive psychology
16:53:17 <ericP> ... gave up and moved to other means
16:53:45 <ericP> [slide 6] The Project for Scientific Psychology
16:54:44 <ericP> ... LTP ideas from circa 1895
16:55:16 <ericP> ... much of our current research still rolling arouund ideas from centuries ago
16:55:32 <ericP> [slide 7] Santiago Ramon
16:55:57 <ericP> Don: Santiago: information flows from axons to dendrites to axons to dendrites
16:56:01 <ericP> ... mostly true
16:56:16 <ericP> [slide 8] [labeled brain]
16:56:26 <ericP> [slide 9] [sections]
16:56:44 <ericP> Don: starts showing differences in patters of cells in areas of the brain
16:57:15 <ericP> ... we're looking at a very gross level
16:57:29 <ericP> [slide 10] [pointelist brain]
16:57:50 <ericP> Don: in neuroscience, your either a lumper or a splitter
16:58:11 <ericP> ... how do we get concensus and get into the details of how the system works?
16:58:36 <mscottm> [Don] pointing to top of slide 10
16:58:40 <ericP> ... "cortex" means "bark"
16:59:29 <ericP> slide 12] [11, with labels]
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17:00:45 <ericP> [slide 12 (guess last was 11a)] gene networks with brain networks
17:01:31 <ericP> don: exampined long range connections in 40s
17:02:00 <ericP> ... (gross connections between brain structures)
17:02:03 <ericP> ... 80% have proven incorrect
17:02:11 <ericP> ... keeps growing
17:02:23 <ericP> [slide 13] Databases and Datasets
17:02:37 <ericP> Don: lots of databases out there now
17:02:55 <ericP> ... seeing useful new techniques, e.g. brainbow
17:03:11 <ericP> [slide 14] New Techniques to See Wiring
17:03:28 <ericP> Don: allows you to see connections in the cells
17:03:59 <ericP> ... gathering data with automated photon microscopes
17:04:09 <ericP> [slide 15] Connectome
17:04:39 <ericP> Don: huge amout of innovation to connect the automated collection with our informatics
17:05:15 <ericP> ... connectome examinines signals on a long range connections
17:05:42 <ericP> [slide 16] Neurophil
17:06:22 <ericP> [slide 17] [purple dye showing intra-cell connections]
17:06:48 <ericP> [slide 18] set of individually traced connections
17:07:01 <ericP> Don: there's growing automation
17:08:05 <ericP> ... proteins in and structure of axons and dendrites all relevent
17:08:38 <ericP> ... processing therein controls how the nerve cell gets info from a to b
17:08:55 <ericP> [slide 19] [more traced connections]
17:09:10 <ericP> [slide 20] [still more traced connections]
17:09:35 <ericP> don: complexity in these microstructure is immence
17:10:20 <ericP> ... illustrations in slide 20 are just cartoons [gross simplifications]
17:10:53 <ericP> [slide 22] Large-Scale Neural Circuit
17:11:11 <ericP> Don: manual tracing would require 10Ks of man-years
17:11:30 <ericP> [slide 23] [microscopy image]
17:12:10 <ericP> Don: this image is on a 20 micron scale (of 3lbs of brain in a human)
17:12:31 <ericP> [slide 24] [Signals in the Neurophil]
17:12:35 <ericP> [slide 25] [Signals in the Neurophil]
17:12:59 <ericP> [slide 26] Activity in Awake Behaving Animals
17:13:14 <ericP> [slide 27] Neuroinformatics Challenge
17:13:28 <ericP> Don: is old new, a montra
17:13:56 <ericP> [slide 28-29] Some Exciting Tech Projects
17:14:11 <ericP> [slide 30] Brain Navigator
17:14:42 <LenaDeus> Brain Navigator: http://www.brainnav.com/
17:14:49 <ericP> Don: saw Elsevier offering Brain Navigator at conf@@3
17:15:05 <ericP> [slide 31] The NeuroNetwork
17:15:19 <LenaDeus> Neuronetwork: theneuronetwork.com
17:15:29 <ericP> Don: Springer offering a Facebook for neuroscientists
17:15:48 <ericP> ... expect useful tool will lie in the middle
17:16:01 <ericP> [slide 32] Summary
17:16:31 <ericP> Don: have so much, how do we apply to a broader audience
17:17:14 <ericP> Micheal, end in site to data growth?
17:17:27 <ericP> Don: exponential growth over 50 years
17:17:45 <ericP> ... Connectome should give us a better sense of "miso-scale" connections
17:18:04 <ericP> ... at the micro-scale, we're at the very beginning
17:18:23 <ericP> ... as with science, we thought that DNA was the end, but now we have RNAa...
17:19:03 <ericP> Kei: thanks for the talk, touch on size and complexity
17:19:16 <ericP> ... are you taking variation into account?
17:19:25 <ericP> ... is this a canonical brain?
17:19:37 <ericP> Harold: should be Vendo's brain
17:19:59 <ericP> Don: Connectome starts with a mouse
17:20:16 <solbrig> Ventner
17:20:20 <nigam> miso-scale --> meso-scale
17:20:42 <ericP> s/miso-scale/meso-scale/
17:21:03 <ericP> s/Vendo's brain/Ventner's brain/
17:21:11 <nigam> Cool! .. i can do regexp
17:21:38 <ericP> Don: a brain structure within the brain is amazingly specific
17:22:15 <ericP> ... stereotypes work; we can find cells in one worm and find corresponding cells in ever other worm
17:23:09 <ericP> ... can use new techniques to get down the the details of e.g. fruit flies and worms
17:23:59 <ericP> ... i think it makes sense to focus on a fly or a worm (though many folks not interested in a work)
17:24:38 <ericP> Alan Hobbs: will a @@5 help us extract variations?
17:24:53 <ericP> ... and help clinicians, etc.
17:25:38 <ericP> Don: e.g. ANDI looks at neurodegeneration over time in alzheimer's patients
17:26:07 <ericP> ... seen how individuals, or [characteristic] groups are important
17:26:31 <ericP> ... don't see many pubs which differentiate a male and female brain
17:27:00 <ericP> ... despite obvious dimorphisms; cells that exist in one or another gender
17:27:48 <ericP> [missed michael miller's comment]
17:28:21 <ericP> Don: usually discussion of sex differences concentrate early hormonal differences
17:29:05 <ericP> ... how able to move genes off of X and Y to differentiate between hormones and physiology
17:29:31 <ericP> mscottm: great article illustrating examining a physical components
17:29:56 <ericP> [slide -- picture of a PC board in a radio]
17:30:10 <LenaDeus> can a biologist fix a radio: http://protein.bio.msu.su/biokhimiya/contents/v69/pdf/bcm_1403.pdf
17:30:11 <ericP> [slide -- picture of a two PC boards in a potentially two radios]
17:30:48 <ericP> [slide -- simple electronics schematic of a radio]
17:31:12 <ericP> mscottm: i don't think it's hopeless for us to discover how brain works by examining components
17:31:40 <ericP> ... we're not looking at the transitors to study transmitted music and culture
17:32:00 <ericP> ... instead we're grouping them to L-C circuit, etc.
17:32:28 <ericP> ... need to share that data across disciplines
17:33:14 <ericP> ... we'd like a SemWeb desc of the components (||- resistors, capacitors, ...
17:33:25 <ericP> ... ).
17:33:39 <ericP> ... want to predict what happens if we change one of these components
17:33:53 <ericP> ... leads to a question:
17:34:07 <ericP> ... .. you said we want to gather data and integrate it
17:34:17 <ericP> ... .. what are the bottlenecks in that process?
17:34:43 <ericP> ... .. are we waiting on anatomical ontologies?
17:35:04 <ericP> ... .. are people at different levels of focus but need to align?
17:35:26 <ericP> Don: so many areas, level of detail varies
17:35:44 <ericP> ... any framework we offer may be proven incorrect
17:36:23 <ericP> ... as informaticians, we need to be flexible to changes in understanding
17:36:58 <ericP> ... at Brainstage, we've worked hard on usability
17:37:05 <ericP> ... is it both usable and fun?
17:37:25 <ericP> ... places like facebook entice folks offer content
17:38:08 <LenaDeus> eric:is there an infrastrucure we can develop to improve people collaborating
17:39:09 <LenaDeus> eric: if we recordd a piece of data on the SW and then new discoveries come along, that is where the SW will prove itself - will data still be useful?
17:39:43 <LenaDeus> eric: should we prove that to the world (data still be useful even though it was incorrect)?
17:40:06 <ericP> mscottm: should we characterize different types of research?
17:40:49 <ericP> ... you have simulation folks, who could try to express e.g. differential equations in RDF
17:40:51 <LenaDeus> BlueBrain: http://bluebrain.epfl.ch/
17:41:17 <ericP> ... when speaking with the BlueBrain folks, you want to speak about components
17:42:00 <ericP> ... you can combine semantic annotations on these components with acquired data [e.g. bulk relational data?]
17:43:30 <ericP> Don: many folks beleive that ultimately we will need mathmatical models to understand the brain
17:43:50 <ericP> ... there was a recent paper mathmatically describing neuron morphology
17:44:14 <ericP> mscottm: trying to see what we should offer; do we need to cater to e.g. modelers?
17:44:51 <ericP> ... there's also the omics viewpoint
17:45:30 <ericP> nigum: are we trying to sell SemWeb tech to solve existing Neuroscience problem? or offering a new system?
17:45:46 <ericP> ... service mindset projects are good fodder for companies
17:46:01 <ericP> ... not as good for impressing folks
17:46:21 <ericP> ... wow factor: we can do something you can never do before
17:46:55 <ericP> mscottm: need to be pragmatic. if a service-oriented opportunity presents, we should consider it
17:47:19 <ericP> ... in 92 i asked "why is there no such thing as bioinformatics?"
17:47:27 <ericP> ... (now terabytes of data)
17:47:52 <ericP> ... a lot of projects will produce lots of data, but there's no point if the data isn't shared
17:48:07 <ericP> ... need to provide for data stewardship
17:49:04 <ericP> ... even in systems biology, proposals offer [clunky] interfaces to e.g. RDBs
17:49:38 <ericP> ... just making data accessible, it's more than they've had
17:49:58 <ericP> Michael: was impressed by SenseLab 'cause it's available today
17:50:12 <ericP> ... SemWeb islands becoming available and connectable
17:50:38 <ericP> ... new RDF tags will help websites become SemWeb-enables
17:51:17 <ericP> mscottm: SemWeb doesn't require same distribution as document web
17:51:34 <ericP> ... SemWeb works well for latent connection of islands
17:51:42 <ericP> ... which islands do we need to connect?
17:52:12 <ericP> Kei: Don showed lots of examples at the end [slides 28-29]
17:52:19 <ericP> ... they're not currently connected
17:52:39 <ericP> ... could allow scientists to ask questions that can't currently
17:52:43 <mscottm> Zakim, who is on the phone?
17:52:43 <Zakim> On the phone I see Susie, HCLSf2f, matthias_samwald
17:53:09 <ericP> ... need to develop ontologies which offer value to neuroscientists
17:53:41 <ericP> Mark Musen: parallel between work on understanding brain function and our informatits work
17:53:57 <ericP> ... big space between meso-level and micro-level
17:54:10 <ericP> ... there's no ontology for systems at this level
17:54:31 <LenaDeus> Mark Musen: ontologies are useless in neuroscience because we don't know about all the structures, let alone how to name them
17:54:35 <ericP> ... could encourage research communities to produce their own onts and then fit them into the bigger picture
17:55:12 <ericP> Allen Hobbs: need a vocabulary in which they can express their questions
17:55:23 <ericP> ... need a forum jsut for the SemWeb
17:55:37 <matthias_samwald> (voices from the 'audience' are a bit difficult to understand through Zakim, in part)
17:55:51 <ericP> Don: most of the folks interested in their one area
17:56:07 <ericP> ... the high-profile folks are interested in e.g. Connectime
17:56:22 <ericP> ... everyone now knows about the SemWeb
17:56:35 <ericP> ... Connectome folks talked about OWL and cited SemWeb
17:56:44 <ericP> ... W3 has gotten this process kick-started
17:57:04 <ericP> ... don't need to market as much as help
17:57:19 <ericP> ... NIF is pulling this info together
17:57:35 <ericP> ... the bulk of folks don't go the informatics posters
17:57:50 <ericP> ... scientists just ask "when can we use it?
17:58:05 <ericP> Allen: how do you get beyond "i want to use it now"?
17:58:32 <ericP> Don: there are informatics meetings at the conferences, but same faces
17:58:55 <ericP> Fahim: within NIF, there are knowledge engineering folks and domain folks
17:59:02 <ericP> ... gap between the two
17:59:10 <nigam> nigam has joined #hcls
17:59:20 <ericP> kei: i still have a hard time explaining URI to Gordon
17:59:50 <ericP> Fahim: Neurolex.org is a wiki format of our core ontology, NIF standard
18:00:13 <ericP> ... currently export OWL ont into a wiki, but no mechanical return
18:00:35 <ericP> ... we have a cell working group who was able to start with small annotations
18:00:49 <ericP> ... (instead of learning a technology)
18:01:29 <ericP> mscottm: how do you use them? outline views? annotate stuff on wiki? SPARQL-able?
18:01:39 <Zakim> -Susie
18:01:44 <ericP> Fahim: neurolex more of a wikipedia environment
18:02:03 <ericP> ... have category pages for ontological concepts
18:02:22 <ericP> ... can explore through tree-like views, or export CSV dumps of the graph
18:02:32 <ericP> ... easier to learn than Protege or DL
18:02:56 <ericP> ... developing simple forms, e.g. info on a neuron in a brain region
18:03:39 <ericP> Harold: i can chat for 15 mins about how Neurolex works
18:03:46 <Zakim> +??P0
18:04:07 <jun> jun has joined #hcls
18:04:19 <ericP> Michael: i like the "can folks use this?" question
18:04:27 <jun> hello everybody:)
18:04:38 <ericP> ... concentration on getting the terminology
18:05:04 <ericP> Michael: doesn't have a business use
18:05:28 <ericP> Harold: if your familiar with wikis and wiki annotation, it gets you RDF triples of that for very low cost
18:05:57 <ericP> ... it's isomorphic to RDFa
18:06:05 <ericP> ... captures knowledge to the extent you have it
18:06:25 <ericP> nigam: look wikipathways
18:06:44 <ericP> ... wiki used for multiple uses of concept annotation capture
18:06:53 <ericP> ... vs. data annotation capture
18:07:52 <LenaDeus> eric: can I do query federation on top the the wikis?
18:07:58 <ericP> ... wikipathway offers a wiki interface but forces use of controled vocabs
18:08:28 <ericP> michael: when i'm doing an experiment, i'd like to see who else is doing that?
18:09:01 <ericP> nigam: wikipathways (UCSF) is similar to wikiprofessional
18:09:20 <ericP> ... wikipathways offers editing of the ontology itself at the same time
18:09:38 <ericP> karen: how can we offer something to help build this community?
18:10:00 <ericP> ... we should think about our communications roll
18:10:23 <ericP> ... we should be conneting more at neuroscience conferences, e.g. BOFs
18:10:28 <nigam> ... wikipathways allows you to edit a pathway in a visual environment that "forces" you to speak in GenMAPP or BioPAX without being bogged down in the syntax for those pathway ontologies
18:10:39 <ericP> mscottm: there are several wiki's have been mentioned in this room
18:11:04 <nigam> ... then it allows you to annotate the captured pathway using terms from several controlled vocabularies (loosely called "ontologies)
18:11:21 <ericP> ... folks in W3 are looking at new semantic wikis, but would be nice to re-use a common framework
18:11:52 <ericP> harold: i think all i've heard of are, or will, be mediawiki
18:12:30 <nigam> ... the paradigm is the same as wikiproffessional (that of using the wiki-platform for collaborative knowledge capture; or for collaborative annotation)
18:12:33 <Zakim> -??P0
18:12:57 <ericP> mark musen: everyone knows how simple it is to use wikipedia
18:13:15 <ericP> ... belies the concept that there are usefully modeled data underneath
18:13:33 <ericP> ... think we need to focus on making complex information viewable/editable
18:14:33 <ericP> harold: a lot of the success of the genome project came from the extensibility of the ASN-1 model
18:14:38 <nigam> ... and have clarity on what is the complex information we are making viewable/editable (the ontologies itself, the data, annotations on those data, the discourse about the conclusions derived from the data and so on)
18:14:53 <nigam>  ... not making the distinction leads to what I call "wikimania"
18:15:39 <mscottm> Hi Matthias, Jun, Susie - taking a 15 min break
18:15:50 <matthias_samwald> okay, thanks
18:16:24 <jun> thanks
18:16:47 <matthias_samwald> I'l drop off the call til then.
18:16:53 <Zakim> -matthias_samwald
18:21:07 <Jeffery> Jeffery has joined #hcls
18:29:17 <Zakim> +Susie
18:29:41 <Susie> Susie has joined #hcls
18:32:10 <Zakim> +??P3
18:32:27 <matthias_samwald> zakim, ??P3 is matthias_samwald
18:32:27 <Zakim> +matthias_samwald; got it
18:35:44 <Zakim> +??P8
18:36:01 <jun> hi scott
18:36:03 <jun> it was Jun
18:36:57 <jun> zakim, +??P8 is jun
18:36:57 <Zakim> sorry, jun, I do not recognize a party named '+??P8'
18:37:09 <jun> zakim, ??P8 is jun
18:37:09 <Zakim> +jun; got it
18:37:18 <andreasplendiani> andreasplendiani has joined #HCLS
18:41:12 <Zakim> +ElgarPichler
18:41:57 <Zakim> +andreassplendiani
18:43:01 <andreasplendiani> Hi, I'm having my mic on mute, but I'm listening
18:43:48 <LenaDeus> we're at break
18:45:21 <andreasplendiani> I hear :)
18:45:30 <jun> you need safari for Mac, I think
18:45:45 <andreasplendiani> Yes, it works with Safari. Had problem with firefox
18:49:44 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-11-02_F2F?action=AttachFile&do=get&target=MarkMusenHCLS2009.pptx Mark's talk
18:50:06 <ericP> topic: Collaborating with the National Center for Biomedical Ontology 
18:51:27 <andreasplendiani> ok, works
18:51:54 <mscottm> Matthias - I'm downloading the pptx and will convert it for you. Shall I put it in .ppt?
18:51:58 <ericP> matthias_samwald, ETA on PDFL 5 mins?
18:52:00 <ericP> 2 mins?
18:52:27 <mscottm> shall I make pdf instead?
18:52:49 <ericP> Mark: invite interruptions inline
18:53:03 <ericP> [slide 2] NIH Roadmap
18:53:50 <matthias_samwald> pdf is okay
18:54:21 <ericP> [slide 3] NIH Roadmap (geographical)
18:54:37 <ericP> [slide 4] NCBO
18:55:07 <ericP> Mark: make ontologies useful, share tools
18:55:17 <ericP> [slide 5] NCBO: Key activities
18:56:00 <ericP> [slide 6] [NCBO Website bioontologies.org]
18:56:11 <nigam> www.bioontology.org
18:56:13 <ericP> Mark: lots of tools for collaboration
18:56:33 <ericP> ... creation of infrastructure, and proseletizing use
18:56:53 <ericP> [slide 7] [bioportal.bioontology.org]
18:57:13 <ericP> Mark: all of the important ontologies
18:57:27 <ericP> ... ... in biomedicine
18:57:38 <ericP> ... can see activity:
18:57:43 <ericP> ... .. recent uploads
18:57:48 <ericP> ... .. annotations
18:57:51 <ericP> ... .. mappings
18:58:05 <ericP> ... developmental ontology has a zillion new mappings
18:58:27 <ericP> ... helps folks where action is
18:58:28 <ericP> ... can subscribe to RSS feed
18:58:49 <mscottm> Mark's talk now is available as pdf (main link).
18:58:51 <ericP> [slide 8] BioPortal allows us ...
18:58:54 <matthias_samwald> thanks
18:59:02 <mscottm> http://esw.w3.org/topic/HCLSIG/Meetings/2009-11-02_F2F?action=AttachFile&do=get&target=MarkMusenHCLS2009.pdf
18:59:30 <ericP> Mark: online mechanism for peer review
18:59:37 <ericP> ... make peer review democratic
18:59:49 <ericP> [slide 9] [bioportal library]
19:00:00 <ericP> Mark: alphabetical list of ontologies
19:00:13 <ericP> ... we are ecumenical about supported onts
19:00:37 <ericP> ... we allow users to filter based on group (e.g. OBO foundry, WHO)
19:00:59 <ericP> [slide 10] [snippit of NCI thesaurus]
19:01:17 <ericP> Mark: fancy animation on right, standard tree browser on left
19:01:49 <LenaDeus> http://bioportal.bioontology.org/
19:02:10 <ericP> [slide 11] Users can view and create mappings
19:02:28 <ericP> Mark: expect to have onts well beyond UMLS
19:02:35 <nigam> http://bioportal.bioontology.org/visconcepts/40644/?id=Skin_Neoplasm#t_tab1:
19:02:54 <ericP> ... have tools which lexically map ontologies
19:03:28 <ericP> ericP: you've spot-checked this for sanity?
19:03:43 <ericP> Mark: yes, sacrified recall for accuracy
19:03:55 <ericP> ... a lot of mappers don't perform
19:04:20 <ericP> Michael: a lot of open source mappers work at toy level
19:04:30 <ericP> mscottm: i think you meed demos
19:04:44 <ericP> Mark: mapping tools which are described at conferences
19:04:56 <ericP> [slide 12] Biomedical Resource Ontology
19:05:24 <ericP> Mark: ontology of algorithms, ontologies, ...
19:05:42 <ericP> ... like a google sitemap but for biomedical community
19:06:00 <ericP> ... BRO developed with collab between NCBO, NIH
19:06:11 <ericP> [slide 13] "Note" in BioPortal
19:06:44 <ericP> Mark: david went through much of the BRO and left "marginal notes"
19:07:29 <ericP> ... have threaded discussions where david and peter argue
19:07:54 <ericP> mscottm: do you use Information Artifact Ontology
19:08:11 <ericP> Trish: can out of a branch of OBI
19:08:24 <ericP> Mark: need to harmonize with that and with NIF
19:08:57 <ericP> ... as with folks who use wikis to comment on ontologies, we use notes, which have more structure
19:09:20 <ericP> ... goal is that ontology developers can look at the discussions and improve the ontology
19:09:34 <ericP> [slide 14] Community-Based Annoataion as Peer Review
19:10:09 <ericP> Mark: expect that users are in the best position to evaluate ontologies
19:11:10 <LenaDeus> eric: Users would contribute comments to improve ontologies because future versions might cover their needs more closely
19:12:12 <ericP> Mark: expect to put TMO up and see if folks leave notes
19:12:26 <ericP> [slide 1] BioPortal is building...
19:12:46 <ericP> s/[slide 1] BioPortal is building.../[slide 15] BioPortal is building.../
19:12:53 <ericP> [Mark sneezes]
19:13:10 <ericP> Mark: helpful to know when new versions will be released
19:13:24 <ericP> ... use not only for browsing but for finding services
19:13:48 <ericP> ... theis functionality is implemented as web services
19:14:08 <ericP> ... (not just [browser-oriented] web interfaces)
19:14:27 <ericP> [slide 16] Word Add-In
19:14:44 <LenaDeus> http://ucsdbiolit.codeplex.com/
19:14:55 <ericP> [slide 17] Word automated recognition of ont...
19:15:27 <ericP> Mark: it uses Bioportal web services (news to us) to do term matching
19:15:49 <ericP> [slide 18] BioLit Web resource...
19:16:08 <jun> what happens if the terms were changed or deleted?
19:16:41 <ericP> Susie: like the word plugin, would like it for excel
19:17:18 <ericP> mscottm: note Anzo (Cambridge Semantics)
19:17:29 <ericP> Susie: need it to be part of a larger tool set
19:18:01 <ericP> Mark: this area has gotten much more crowded since we got our NIH grant
19:18:23 <ericP> [slide 19] IO informatics
19:18:59 <ericP> Mark: give access to heterogeneous data sources, including stuff indexed in bioportal
19:19:11 <ericP> [slide 21] Ontology Tags
19:19:27 <ericP> Mark: makes sure folks are using appropriate terms on the wiki
19:19:49 <ericP> [slide 22] ISAcreator
19:19:55 <ericP> Mark: comes from EBI
19:20:08 <ericP> ... downloads onts from BioPortal and EBI
19:20:25 <ericP> Michael: mostly for omics and multi-omics
19:21:00 <ericP> ... we're working on a similar tool
19:21:10 <nigam> ... ISA_creator uses the search service as well
19:21:12 <ericP> [slide 23] ECG Gadget
19:21:32 <nigam> All services accessed by these tools are at: http://www.bioontology.org/wiki/index.php/NCBO_REST_services
19:21:48 <ericP> Mark: take a digitized ECG and annotate it with onts found at bioportal
19:22:26 <ericP> [slide 24] Biositemaps editor
19:22:46 <ericP> Mark: when folks enter info on a resource, they try to use controlled terms
19:23:16 <ericP> ... looks at the relevent ontology and integrates terms from the BRO directly into the webpage
19:23:49 <ericP> ... controled web page input theme shows up in this site and Gadget
19:24:14 <ericP> [slide 25] Protégé BioPortal...
19:24:26 <ericP> [slide 26] Simbios
19:24:28 <nigam> The general theme is that we provide REST services to access, download, traverse, search, visualize and refer to ontologies and ontology terms
19:24:35 <ericP> Mark: used to model everything
19:25:29 <ericP> ... our BioPortal widgets give you tools to autocomplete
19:25:58 <ericP> ... having a hard time seeing who's using it
19:26:29 <ericP> ... we don't want to be in the customer support business, or be intrusive, but we need to justify our funding to NIH
19:26:59 <ericP> ... have seem annotations applied to acquired data
19:27:14 <ericP> ... looking at automating annotating experimental data
19:27:28 <ericP> [slide 27] NCBO Annotator
19:27:51 <ericP> [slide 27 build 2] NCBO Annotator...
19:28:21 <ericP> Mark: want to take embedded natural language and do term resolution/disambiguation
19:28:32 <ericP> [slide 28] NCBO Annotator
19:29:10 <ericP> Mark: want to analyze text and get a term cloud
19:29:33 <ericP> [slide 29] Resource Index
19:29:37 <nigam> more on the annotator at: http://www.biomedcentral.com/1471-2105/10/S9/S14/abstract
19:30:17 <ericP> Mark: allows us to search online for related datasets or do datamining from data sets
19:30:35 <nigam> more on the resource index at: http://www.biomedcentral.com/1471-2105/10/S2/S1
19:30:35 <ericP> [slide 30] Example: Indexing GEO
19:30:48 <ericP> [note builds]
19:31:41 <ericP> [slide 31] [NCI thesaurus again]
19:32:16 <ericP> Mark: can match terms for melanoma, but not "skin cancer"
19:33:19 <ericP> ... brings you directly from ontologies to data
19:33:55 <ericP> kei: got a list of gene lists ...
19:34:19 <ericP> nigam: in previous HCSL presentation i showed xml
19:34:28 <Karen> Karen has joined #hcls
19:34:36 <Zakim> +??P6
19:34:39 <ericP> Mark: annotation has become a big bisiness
19:34:51 <nigam> Talk with XML outputs of services: http://bioportal.bioontology.org/visualize/40644
19:34:57 <ericP> [slide 32] GMiner
19:35:04 <nigam> oops .. this one: http://www.stanford.edu/~nigam/cgi-bin/dokuwiki/doku.php?id=download
19:35:25 <ericP> [slide 35] See our wiki
19:36:03 <mscottm> http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project
19:36:04 <ericP> http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project
19:36:24 <ericP> [slide 36] way to collaborate
19:36:36 <ericP> Mark: you can be a driving bilogical project
19:36:55 <ericP> ... use our grant to offer challenges
19:37:13 <ericP> ... need sweet point between one DBPs and too many DBPs
19:37:25 <ericP> ... can also write NIH research grants
19:37:48 <ericP> ... have had some industrial grants
19:38:03 <ericP> [slide 37] Current DBPs
19:38:18 <ericP> Mark: had to pick 3 of 9 excellent candidates
19:39:00 <nigam> Link to "invasive skin neoplasm" concept to see the visualization tools http://bioportal.bioontology.org/visconcepts/40644/?id=Invasive_Melanoma#t_tab1:
19:40:23 <ericP> Mark: has created a Sesame Street for ontolgies
19:40:40 <ericP> [slide 38] Current "collaborating R01" grants
19:41:55 <ericP> Mark: funding rate is around 80%
19:42:12 <ericP> ... $250-$500K annually
19:42:21 <ericP> ... 3-5 years
19:42:29 <ericP> ... usual annual report
19:43:05 <ericP> ... stimulus funding requires quarterly
19:43:53 <ericP> mscottm: contacts with cleaveland clinic?
19:44:05 <ericP> ... Mark Wilkinson (UBC)?
19:44:35 <ericP> Mark: don't know if the cardio folks are reaching out to cleveland clinic or UBC
19:45:32 <ericP> ... don't need to be an academic to collaborate
19:45:57 <ericP> ... nextbio, google, colbix (SP?)
19:46:06 <ericP> ... google funding web-o-trust
19:46:56 <ericP> ... ontology metadata v @@6
19:47:31 <mscottm> http://ontoware.org/projects/omv/
19:47:37 <ericP> [slide 40] other NCBO components
19:48:11 <ericP> [slide 41] NCBO needs HCLS
19:48:13 <mscottm> http://www.google.com/url?sa=t&source=web&ct=res&cd=2&ved=0CA4QFjAB&url=http%3A%2F%2Fwww.neon-project.org%2Fweb-content%2Fimages%2FPublications%2Fneon_2009_d832.pdf&ei=GjfvSrfzJ4qOswO3ofHhBw&usg=AFQjCNEr5tXE7PoBDFJcw08-UKoQ_ElSWw&sig2=wPF_fux73UzoIAlq2DqYGQ
19:48:33 <ericP> Mark: need you guys to use our tech and drive our requirements 
19:48:37 <mscottm> http://neon-toolkit.org/wiki/Main_Page
19:48:43 <ericP> ... use HCLS for proseletizing
19:49:03 <nigam> ... come to the ISMB Bio-ontology SIG to show your work!
19:49:05 <ericP> ... frustrated that W3C recommendations aren't having the traction we'd like
19:50:15 <ericP> lena: if you have an affymetrix micro array, we can plug in a matlab a compontent to get ups and downs automatically
19:50:26 <ericP> ... any term set for such workflow detail?
19:50:49 <ericP> nigam: cytobank is using terms from maybe 25 terms
19:51:22 <ericP> michael: we didn't do it formally; we used apt tools or matlab, but we never thought to hook them up to terms
19:51:53 <ericP> nigam: if someone uses taverna, you can terms from us, algorithms from someone else
19:52:07 <ericP> Mark: had conversation with Carol Goble about this
19:54:06 <ericP> lena: rather than pushing data to the analysts, why not push the tools to the biologists?
19:54:42 <ericP> mscottm: missing experimental conditions as ontologies
19:55:57 <ericP> LenaDeus: protocols which the machine controls are pretty standard
19:56:23 <ericP> mscottm: one of the biggest factors of microarray data is the folks who did the clustering
19:58:15 <ericP> ... most people are stuck just on trying to find corresponding experiements
19:59:19 <ericP> -> http://en.wikipedia.org/wiki/MammaPrint MammaPrint
19:59:33 <ericP> topic: Discussion: Alignment with NCBO (including ISMB SIG) 
19:59:45 <ericP> mscottm, obvious thing is to incorporate your services into our demos
20:00:14 <ericP> nigam: will be offering RDF exports of as many ontologies as we can
20:00:26 <andreasplendiani> RDF export of REST services!
20:00:29 <ericP> ... it will be bio2rdf, but you can tweak the namespace
20:01:54 <ericP> ... how do we plug in our ontology content and reource annotation services [into hcls demos]?
20:02:11 <ericP> ericP: i think you need to attack our use cases 'cause most of what we do is driven by use case
20:02:19 <nigam> RDF exports of ontology-content
20:08:08 <ericP> mscottm: you want to start sharing work at the differentially expressed gene sets
20:10:12 <Karen> +1 Matthias!
20:10:27 <ericP> mscottm: part from gene lists, matthias_samwald uses obo ontologies in his atags work
20:10:43 <ericP> ... would it be useful to access the NCBO services?
20:10:55 <ericP> matthias_samwald: been on the todo list
20:11:07 <ericP> ... was waiting for the OWL version of NCBO services
20:12:13 <ericP> ... the current OWL is very complicated (property restrictions), and the URIs don't match the official obo terms
20:12:46 <ericP> nigam: you're using a prototype
20:13:29 <ericP> ... our production is just XML 'cause folks have a hard time using the OWL which would require anonymous classes
20:13:37 <andreasplendiani> What about having output in RDF ?
20:14:01 <ericP> s/just XML/domain-specific XML/
20:14:26 <nigam> Do not use the output of the prototype services!!
20:14:40 <ericP> matthias_samwald: might look good in Protégé, but hard to use
20:14:48 <nigam> All production services are at: http://www.bioontology.org/wiki/index.php/NCBO_REST_services
20:15:20 <ericP> ... happy with a subset of the info, e.g. a list of URIs
20:15:35 <andreasplendiani> Would be nice to have the results in RDF :) (it's not difficult to convert, true...)
20:15:43 <nigam> Need to get full URIs in results
20:16:29 <nigam> Andrea, would you be willing to look at the current XML and propose the RDF you would want
20:16:46 <andreasplendiani> I'll have a look
20:17:46 <ericP> ACTION: nigam and matthias_samwald to work out URIs in OWL format
20:19:37 <ericP> Susie: could collab on BioOntologies SIG at ISMB
20:20:01 <ericP> ... good opportunity for HCLS to support the SIG
20:20:45 <ericP> nigam: want to steer the SIG towards solving real probs rather than find-grained discussion of terms
20:21:48 <andreasplendiani> bye. Not sure I can login later.
20:21:55 <Zakim> -Susie
20:21:57 <Zakim> -jun
20:21:58 <jun> bye everybody. Have a good lunch
20:22:00 <Zakim> -ElgarPichler
20:22:02 <Zakim> -matthias_samwald
20:22:04 <andreasplendiani> (dinner)
20:22:08 <andreasplendiani> andreasplendiani has left #HCLS
20:22:17 <Zakim> -andreassplendiani
20:23:52 <Zakim> -??P6
20:38:33 <Zakim> +??P1
20:38:52 <Zakim> -??P1
21:23:20 <Zakim> +Susie
21:24:08 <Zakim> -Susie
21:31:49 <Zakim> +Susie
21:31:50 <ericP> Zakim, who is here?
21:31:50 <Zakim> On the phone I see HCLSf2f, Susie
21:31:50 <Zakim> On IRC I see Susie, egonw, LenaDeus, RRSAgent, Zakim, matthias_samwald, Cloud, ericP
21:31:58 <ericP> hye, susie is here
21:32:24 <egonw> hi ericP, Susie
21:34:04 <Zakim> +ElgarPichler
21:41:49 <LenaDeus> scott: we don't know how huntington disease works, even though we know the gene
21:42:05 <LenaDeus> having lots of data has not helped understand the mechanism
21:42:13 <masao> masao has joined #hcls
21:42:36 <LenaDeus> data stewardship: doing what we can with the data, not just assembling massive quantities of it!
21:43:10 <ericP> -> http://esw.w3.org/topic/HCLSIG/Meetings/2009-11-02_F2F?action=AttachFile&do=get&target=StateOfHCLS.ppt State of the Interest Group: HCLS
21:44:02 <ericP> [slide Knowledge Capture]
21:44:41 <nigam> nigam has joined #hcls
21:44:43 <LenaDeus> the way knowledge is extracted from the wet lab is very different from extraction from papers
21:45:19 <mm> mm has joined #hcls
21:46:11 <allen> allen has joined #hcls
21:47:40 <matthias_samwald> you have not started yet, did you?
21:48:13 <matthias_samwald> oh sorry, now i see new messages. ooops.
21:48:30 <mm> mm is michael miller
21:48:59 <Zakim> +??P3
21:50:36 <Karen> Karen has joined #hcls
21:50:41 <Karen> scribenick: karen
21:50:52 <Karen> Scott: Our current task forces
21:50:54 <Karen> ...there are sic
21:50:58 <Karen> s/six
21:51:10 <Karen> ...BioRDF will be focus tomorrow
21:51:26 <Karen> ...Clinical Observations Interoperability (COI) will give presentation at AMIA
21:51:36 <Karen> ...why they could not be here
21:51:46 <Karen> ...Linking Open Drug Data
21:52:05 <Karen> ...Scientific Discourse is related to soft knowledge we were discussing before
21:52:19 <Karen> ...when people enter a comment into a blog and you want to relate to ontologies and raw data
21:52:33 <Karen> ...Explain the knowledge base
21:52:49 <Karen> ...We wanted to ask a scientific question relevant to data for that question
21:52:56 <Karen> ...We got input from the Alzheimer's Forum
21:53:22 <Karen> ...Drugable targets; signal transduction pathways 
21:53:35 <Karen> ...we assembled a number of heterogeneous data sets
21:53:39 <Karen> ...using RDF and OWL
21:53:46 <Karen> ...coupling different sources by choosing same names
21:53:54 <Karen> ...like "genes" and so forth
21:53:59 <Karen> ...used permanent URLs
21:54:09 <Karen> ...the main work was designing that coupling among the different data sources
21:54:24 <Karen> ...The query was fairly complex
21:54:38 <Karen> ...To flesh out restriction classes, to get to sub classes part of the process
21:54:48 <Karen> ...we did pre-inferencing and added entailments to the graph
21:54:53 <Karen> ...so we could ask questions
21:55:05 <Karen> ...Question went across a number of data sets
21:55:11 <Karen> ...and then out came 42 genes
21:55:19 <Karen> ...And AlzForum said it was a great list
21:55:29 <Karen> ...Unlike Google where you came up with 225K hits
21:55:35 <Karen> ...So we have that knowledge base now
21:55:39 <Karen> ...We are building on it
21:55:45 <Karen> ...It is hosted by DERI Galway
21:56:16 <Karen> ...and Adrian Paschke in Berlin
21:56:33 <Karen> ...Also working on query federation
21:56:37 <Karen> ...and there was recently a publication
21:56:41 <csma> csma has joined #HCLS
21:56:43 <Karen> ...in BioInformatics
21:56:51 <Karen> ...where we discussed a combined effort
21:56:59 <Karen> ...looking at federating resources
21:57:05 <Karen> ...applying SemWeb library resources
21:57:18 <Karen> ...will be a great "magic bullet" with a SPARQL query
21:57:27 <Karen> ...different terminology than what's stored in SQL
21:57:38 <Karen> ...storing terminology and talking to relational databases
21:57:55 <Karen> ...Traditional Chinese medicine is part of our triple store federation
21:58:07 <Karen> ...Looking to how that can be used to address problems
21:58:10 <Karen> ...Linking Open Drug Data
21:58:28 <Karen> ...I think you are aware of this one
21:58:44 <Karen> ...differences between document oriented and assertion oriented
21:58:48 <Karen> ...LODD sets
21:58:56 <Karen> ...that have been produced by these activities
21:59:11 <Karen> ...Look at bottom area of the linked data cloud, is all HCLS data
21:59:23 <Karen> ...So it accounts for quite a lot of the LOD data being served up
21:59:35 <Karen> ...I asked Kinsgley Idehan what he considered to be large
21:59:41 <Karen> ...they are serving 7.5 billion triples
21:59:48 <Karen> ...We have moved from millions to billions
21:59:54 <Karen> ...Doesn't mean you can reason over it
22:00:00 <Karen> ...But you can store it and query it
22:00:02 <Karen> ...Ontotext
22:00:09 <Karen> ...at BioIT World talked about what they have
22:00:25 <Karen> ...Ontotext has something like 15 billion before they added tail mix and inferencing
22:00:29 <Karen> ...which moves to 20 bil
22:00:34 <Karen> ...Four Store
22:00:38 <Karen> ...Teratriples
22:00:46 <matthias_samwald> 4store
22:00:47 <Karen> ...Triple stores have gotten quite large
22:00:59 <Karen> ...Uniprot accounts for quite a lot of triples
22:01:10 <Karen> ...Descibed how many triples they process in three weeks
22:01:14 <Karen> ...on order of 3 billion
22:01:20 <Karen> ...Get the idea
22:01:42 <Karen> ...Clinical Operability TF is going strong
22:01:52 <Karen> ...It's work is being shown at AMIA
22:02:00 <Karen> ...It bridges CDSC to HL7 formats
22:02:06 <Karen> ...Eric can talk more about this
22:02:20 <Karen> ...Looking for patients who are eligible for certain clinical trials
22:02:27 <Karen> ...drug companies now have to do foot work
22:02:40 <Karen> ...to look for clinical trial people
22:02:57 <Karen> Eric: Kaiser Permanente does a good job with this data
22:03:39 <Karen> Scott: This demo takes data sets and puts in proper formats
22:03:58 <Karen> Eric: Relational database with hospital data
22:04:04 <Karen> ...HL7 is one view of that
22:04:18 <Karen> ...another view is to ask a CDSC query
22:04:29 <Karen> ...so it pushes queries all the way back to data base
22:04:35 <Karen> ...ontological agility
22:04:42 <Karen> ...without performance issues
22:04:43 <Zakim> -Susie
22:04:49 <Karen> ...don't have to marterialize it
22:05:13 <Karen> Scott: This "precipitous gap" between the CDSC expression of elibility and what HL7 can consume
22:05:18 <Karen> ...So take an inclusion criterion
22:05:31 <Karen> ...and translate into a tripe (meformin}
22:05:40 <Karen> ...so we can create a triple to represent that constraint
22:05:48 <Karen> ...SPAQRL query includes that constraint
22:06:00 <Karen> Eric: There is backing material now
22:06:13 <Karen> ...a Web interface that Helen Chen and Holgar Pichlar put together
22:06:24 <Karen> ...so you can include exclusionary numbers
22:06:43 <Karen> ...you can abstract, not just brand name drug
22:06:48 <Karen> ...It's a realistic usage now
22:06:56 <Karen> Scott: This is how we perform negation
22:07:03 <Karen> Eric: I'll talk about SPARQL later today
22:07:13 <Karen> Q: Is option an outer join?
22:07:17 <Karen> Eric: yes
22:07:31 <Karen> Scott: Eric mentioned this drug ontology that's incorporated into the Web interface
22:07:39 <Karen> ...so you can check out the demo live on the server
22:07:44 <Karen> ...In the Terminology Task Force
22:07:51 <Karen> ...links to the BioRDF and federation 
22:07:55 <Karen> ...relate features to data
22:08:07 <Karen> ...In various domains, there is a way to relate data to the domains and feature sets
22:08:12 <Karen> ...Text mining and features sets
22:08:16 <Karen> ...gene expression and profiles
22:08:29 <Karen> ...When you have pattern recog algorithms for a domain
22:08:34 <Karen> ...you can classify particular concepts
22:08:43 <Karen> ..good for automated annotation
22:08:54 <Karen> ...People have done things with ontology, Go, and so forth
22:09:06 <Karen> ...In Terminology TF, we decided to employ SKOS
22:09:10 <Karen> ...and not OWL
22:09:15 <Karen> ...Peter can tell us more about that tomorrow
22:09:21 <Karen> ...So we represented SnoMed in SKOS
22:09:34 <Karen> ...There were some Web services that could deal with SKOS out of the box
22:09:42 <Karen> ...AIDA, so we could browse the contents
22:09:54 <Karen> ...John Madden from Duke Univ. showed this at CSHALS conference this year
22:10:09 <Karen> ...Can drag up and have associated labels searched
22:10:15 <ericP> [slide SNOMED CT/SKOS]
22:10:21 <Karen> ...And another view 
22:10:25 <ericP> [slide next one afer that]
22:10:39 <Karen> ...Taking it a step further in the federation work
22:10:49 <Karen> ...We were able to directly connect to HCLS knolwedge base at DERI
22:10:52 <Karen> ...then you could browse
22:11:00 <Karen> ...See Go and ? activity
22:11:19 <Karen> ...If you want to create a SPARQL query, which most people do with data bases
22:11:30 <Karen> ...It's hard to write a query if I don't know what's in the knowledge base
22:11:36 <Karen> ...So do knowledge complemtion
22:11:39 <Karen> ...It finds it via label
22:11:45 <masao> i an not open the StateOfHCLS.ppt .. only my problem?
22:11:57 <Karen> ...When you add to query, see it has a PURL URL
22:12:00 <ericP> [slide Access to triples in Taverna]
22:12:08 <Karen> ...Taverna via AIDA plugin
22:12:21 <Karen> ...We want to make it easy to do so it's unavoidable
22:12:26 <Karen> ...to make a semantic workflow
22:12:37 <Karen> ...take a concept and drag it to your workflow
22:12:43 <Karen> ...and say the data coming from here is a gene list
22:12:52 <Karen> ...gene list is a data type defined in OWL, for example
22:13:16 <Karen> ...Just to get the idea, you can drag a label and tag your label
22:13:23 <Karen> ...so access from within the workflow itself
22:13:30 <Karen> ...If something is an integer, which is all you know
22:13:41 <Karen> ...that it's also a chromosome number
22:13:54 <Karen> ...unless you use Biomoby
22:14:11 <Karen> ...This business of pointing at whatever machine is hosting the instance
22:14:26 <Karen> ...HCLS knowledge base is Virtuoso
22:14:47 <Karen> ...Go to these links
22:15:08 <Karen> ...More accomplishments that you can see
22:15:22 <Karen> ...We have gone millions to billions; the LOD cloud is large
22:16:40 <Karen> ...A few months ago a colleague and I gave a course, half of which was SemWeb
22:17:04 <Karen> ...to bio informatics PhD students, so times are changing
22:17:19 <Karen> ...If we can get to point where some of us are using shared names for obvious things, that would be good
22:17:53 <Karen> ...Concept alliance
22:18:32 <Karen> ...The IG itself has six task forces
22:18:40 <Karen> ...Maybe a philosophical question, but a reality
22:18:44 <Karen> ...six TFs is a lot
22:18:57 <Karen> ...Would also like to reach out the Asia
22:19:12 <Karen> ...Europe and America have active participants
22:19:56 <Karen> ...The times of day in Asia have been difficult
22:20:02 <Karen> ...and how many resources to spread around
22:20:08 <Karen> ...It takes overhead to collaborate
22:20:16 <Karen> Kei: And some people join multiple groups
22:20:31 <Karen> Scott: Eric, Susie, and I try to spread ourselves across the groups
22:20:40 <Karen> ...and it's great that we can integrate across the TFs
22:20:46 <Karen> ...I hope to see that continue
22:21:02 <Karen> ...I would like to mention this concept that Mark Musen brought across
22:21:15 <Karen> ...If you provide your knowledge and your algorithms as services
22:21:25 <Karen> ...then it allows people to create applications based on those services
22:21:38 <Karen> ...so they get the best verion or release and create agile solutions
22:22:01 <Karen> ...I saw an application that incorporates the BioPortal ontologies in a JAVA app
22:22:06 <Karen> ...and I showed you AIDA
22:22:13 <Karen> ...and we talked about HCLS
22:22:24 <Karen> ...If you have to compile code, it becomes too much overhead to colllaborate
22:22:39 <Karen> ...A SPARQL end point on every talbe
22:22:46 <Karen> ...like a "chicken in every pot"
22:22:57 <Karen> ...If you had a SPARQL end point for Uniprot
22:23:00 <Karen> ...which they would like
22:23:10 <Karen> ...and you have SWAN/SIOC
22:23:25 <Karen> ...and myexperiment
22:23:45 <Karen> ...you could link to workflows
22:23:49 <Karen> ...if you expose RDF
22:24:02 <Karen> ...and these various bioinformatics resources and wikis then you can link together with ontologies
22:24:08 <Karen> ...of course the wiki being more than a wiki
22:24:14 <Karen> ...Not just a page everyone can edit
22:24:20 <Karen> ...Two different things come to mind
22:24:30 <Karen> ...A wiki page could be a view into a knowledge base generated by a template
22:24:38 <Karen> ...and the template edited by people who want to change the view
22:24:50 <Karen> ...The source of info 
22:24:59 <Karen> ...if you are able to site a particular resource
22:25:11 <Karen> ...you can create and environment where people site each other and give credit
22:25:21 <Karen> ...this new publishing era that people are discussing
22:25:33 <Karen> Eric: You may want to mention Workshop
22:25:41 <Karen> Scott: We just had a Workshop in Wash, DC
22:25:44 <Karen> ...very successful
22:25:49 <Karen> ...fascinating converations
22:25:55 <Karen> ...at ISWC, great presentations
22:26:05 <Karen> ...put it on irc here
22:26:19 <Karen> ...One of central themes was soft facts as an assertion
22:26:29 <Karen> ...Something that's not an assertion in a knowledge base
22:26:40 <Karen> ...but uses literature or something and you want to use that
22:26:52 <Karen> ...so provide knowledge provinence
22:26:56 <ericP> -> http://esw.w3.org/topic/HCLS/ISWC2009/Workshop WORKSHOP ON SEMANTIC WEB APPLICATIONS IN SCIENTIFIC DISCOURSE
22:26:59 <Karen> ...Like the SWAN forum, for example
22:27:17 <Karen> ...So if I know that group does good research in Alzheimers, then I may cite that
22:27:27 <Karen> ...This use case for a Semantic Wiki
22:27:33 <Karen> ...Because you can query across multiple wikis
22:27:40 <Karen> ...if they provded these services
22:28:01 <Karen> ...and a user said something about Drug A having a side effect; and side effect similarity with Drug B
22:28:10 <Karen> ...and boost theory 
22:28:28 <Karen> ...Drugs with similar side effects have similar targets
22:28:31 <Karen> ...So final slide
22:28:34 <Karen> ...What do we need
22:28:42 <Karen> ...Data stewardship; we need a change of attitude
22:28:58 <Karen> ...The reviewers will hopefully start giving priority to proposals that talk about long-term access
22:29:08 <Karen> ...pay more attention to data colleciton, not just provide an interface
22:29:12 <Karen> ...talk abut how they will do it
22:29:17 <Karen> ...We also need identifiers
22:29:29 <Karen> ...Unclear to me if we have standard identifiers for the most mundane things
22:29:33 <Karen> ...that we can rely on
22:29:38 <Karen> ...so everyone agrees on
22:29:50 <Karen> ...Also scalable triple stores so we can reason in place
22:29:54 <Karen> ...SemWeb isn't magig
22:29:57 <Karen> s/magic
22:30:14 <Karen> ...Maybe we can be satisfied with lightweight or incomplete reasoning
22:30:23 <Karen> ...accept that I am only 70% finished across a graph
22:30:36 <Karen> ...And we need to coordinate and cooperate across the groups doing all the work
22:30:47 <Karen> ...Would like to come out of this meeting with concrete action items
22:30:54 <Karen> ...Align on the metalevel
22:31:05 <Karen> ...and make sure we are complementing and reusing each other's work
22:31:13 <Karen> ...So that's the state of the Interest Group
22:31:17 <Karen> ...Happy to hear comments
22:31:28 <Karen> ...Coordination and cooperation across groups leads into the next topic
22:31:32 <Karen> ...About outreach 
22:31:37 <Karen> ...and how to get more out of less
22:32:01 <Karen> Howard: not sure how to say this
22:32:12 <Karen> ...What impressed me about this community is the wealth of tools and resources available
22:32:18 <Karen> ...and how isolated they seem to be
22:32:23 <Karen> ...COI group connections
22:32:27 <Karen> ...and caBIG community
22:32:39 <Karen> ...It does boggle me how little I see these resources included in grants and places
22:32:45 <Karen> ...where they can benefit from them the most
22:32:51 <Karen> ...I work with National Cancer Institute
22:32:58 <Karen> ...this may seem too advanced to them
22:32:59 <Karen> q+
22:33:11 <Karen> ...but what do we do so we can start using all this tuff
22:33:23 <Karen> ...I see you, Mark[looks at Mark Musen]
22:33:39 <Karen> Nagin: What is good for one may be disastrous for others
22:33:48 <Karen> Mark: You may be right that some are scared of this
22:33:58 <Karen> ...I think SemWeb community has done good job of outreach
22:34:10 <Karen> Howard: I would like to see some of work done in grant proposals
22:34:22 <Karen> Scott: I mentioned some of European partners
22:34:24 <masao> q+ what area enginer want to attend from Japan or Asia? 
22:34:35 <masao> q+
22:34:40 <Karen> ...I would include more from States in these projects if I could
22:34:59 <Karen> ...Idea is to provide data to neuroscientists
22:35:04 <Karen> ...by means of good search support
22:35:15 <Karen> ...instead of using traditional techniques only
22:35:26 <Karen> ...you cannot ignore data warehousing; it works well for some situations
22:35:35 <Karen> ...will always be another data warehouse you need to include
22:35:40 <Karen> ...use for the small stuff
22:35:46 <Karen> ...some data is growing rapidly
22:35:53 <Karen> ...leave where it is, federate it
22:36:07 <Karen> Howard: My perception that it's not being used; that it's isolated?
22:36:14 <Karen> Mark: There is some isolation
22:36:22 <Karen> ...caBIG has isolated itself
22:36:26 <Karen> ...and OMG is in another world
22:36:30 <Karen> Howard: Yes, I know that
22:36:47 <Karen> Mark: You have more contacts with these other orgs to put toe in water
22:36:59 <Karen> ...OMG has put forward with a special interest group
22:37:03 <Karen> ...starting to bring awareness
22:37:13 <Karen> Mark: The case to developers stuck with UML
22:38:17 <Karen> Karen: W3C is speaking with caBIG representatives
22:38:21 <Karen> ...have some IP questions
22:38:31 <Karen> HOward: caBIG said they don't do triple stores
22:38:45 <Karen> ...in that area one of things that needs to happen is an active educational session
22:38:51 <Karen> ...run software to disprove myths
22:39:03 <nigam> Who are the caBIG representatives participating in the discussions?
22:39:11 <Karen> Mark: What's fair to say...is that industry is looking at SemWeb
22:39:15 <Karen> s/Howard/Harold
22:39:24 <Karen> Harold: Stonebreaker 
22:39:35 <Karen> Q: was he going to column data bases
22:39:42 <Karen> ack Masao
22:39:46 <Karen> ack Karen
22:39:53 <Karen> Masao: I am interested in this area
22:40:03 <Karen> ...What kind of engineer or researcher do you want to join from Asia
22:40:12 <Karen> ...drug person
22:40:16 <Karen> ...drug company person
22:40:17 <nigam> Q: Who are the caBIG representatives participating in the discussions?
22:40:24 <Karen> Scott: Somebody who will bring a programmer with them
22:40:41 <Karen> ...so someone who can apply programming, since it's one of the bottlenecks
22:40:50 <Karen> ...I have been waiting for years for some things
22:41:10 <Karen> Scott: Need a clear idea of what they want to get; someone who has data
22:41:49 <Karen> Eric: Need relevance 
22:42:43 <Karen> Scott: We can make extra teleconferences to try to work it out
22:43:07 <Karen> Scott: So RO1, in US
22:43:12 <Karen> ...from Mark
22:43:19 <Karen> Mark: Europeans can apply, but harder
22:43:34 <Karen> Mark: Lots of ways people in this room and community could benefit from some of services we have
22:43:38 <Karen> ..raise the number of believers
22:43:45 <Karen> ...it's in everyone's interest
22:43:57 <Karen> ...NIH has not been favorable toward grants involving software engineering
22:44:07 <nigam> More at: http://www.bioontology.org/how-to-collaborate
22:44:09 <Karen> ...One mechanism would be one of these collaborating projects
22:44:27 <Karen> Kei: Ooes NIH fund community work?
22:44:35 <Karen> ...NSF does community based
22:44:40 <Karen> Mark: It's unual 
22:44:51 <Karen> ...are some special requests to create consortia, but those are rare
22:45:10 <Karen> Scott: Along similar lines, EPI is interested in SemWeb approaches
22:45:15 <Karen> ...Eric and I talked to them about it
22:45:22 <Karen> ...about the gene atlas
22:45:28 <Karen> ...exposing as RDF
22:45:30 <matthias_samwald> s/EPI/EBI
22:45:59 <Karen> ...This is a myth that people think going for SemWeb is a choice between RDF and Rel databases
22:46:11 <Karen> ...It's possible to do both an complement each other
22:46:17 <Karen> ...data warehousing and federation
22:46:53 <Karen> Q: From a relational data base, you can flip back into an RDF representation on the fly
22:46:59 <Karen> Scott: Yes, that's what Eric was there for
22:47:06 <Karen> ...he has written software to do that
22:47:26 <Karen> Part of caBIG is caArray
22:47:30 <Karen> ...I work with both groups
22:47:33 <Karen> ...Anatar
22:47:36 <Karen> ...From HTab
22:47:43 <Karen> ...Let's you produce your files
22:48:00 <Karen> ...caArray is interested in people accessing their cancer gene expression experiments
22:48:13 <Karen> Scott: There were two people who attended caBIG in March
22:48:26 <Karen> Harold: Gilberto Fragosio
22:48:34 <Karen> Trish: Dave Howe
22:48:44 <Karen> Scott: They were also there for shared names
22:48:49 <Karen> Harold: Primary attraction for some
22:49:05 <Karen> ...original health care identifier morphed into HCLS
22:49:17 <Karen> Josh: There is ongoing interest in caBIG community to apply SemWeb tech
22:49:28 <Karen> ...not make it an either or choice, but a complement
22:49:39 <Karen> EricP: A certain amount of infrastructure you need to invest
22:49:54 <Karen> ...convince them that the "SemWeb hippies" will have some longevity
22:50:10 <Karen> Jeff Abbott: I come from systems engineering background and human decision factors background
22:50:17 <Karen> ...It's just hard to get people to change
22:50:20 <Karen> ...has to have a demo
22:50:24 <Karen> ...proof is in the pudding
22:50:28 <Karen> ...I would like to help with that
22:50:47 <Karen> ...In San Diego, they are fighting about whether to call themselves systems engineers or enterprise architects
22:50:52 <Karen> ...I would love to do a demo
22:50:57 <Karen> ...I am building an HSI template
22:51:05 <Karen> ...It's mandatory
22:51:08 <Karen> ...I'm building a template
22:51:14 <Karen> Scott: SemWeb also has another myth
22:51:27 <Karen> ...that people think about having some giant cloud of ontology
22:51:31 <Karen> ...before you can do something
22:51:38 <Karen> ...Whereas a software engineering approach
22:51:53 <Karen> ...A guy from AstraZeneca, was talking about knowledge management
22:51:57 <Karen> ...he talked about policy level
22:52:05 <Karen> ...and how hard it was to share info inside the organization
22:52:15 <Karen> ...I asked if he would implement on a SemWeb basis
22:52:18 <Karen> ...and share outside
22:52:20 <Karen> ...He was for it
22:52:32 <Karen> ...A lot of people at that level don't think about that aspect
22:52:41 <Karen> ...SemWeb as an interoperability layer
22:52:51 <Karen> ...it's not obvious to everybody, esp. those thinking about policies
22:53:06 <Karen> jeff: They may be thinking about other misgivings; you should ask them
22:53:16 <Karen> Scott: In pharma, you need to have access control
22:53:23 <Karen> ...Eric has presented an approach
22:53:28 <Karen> ...control who can access what data
22:53:39 <Karen> ...by injecting user certificates into the query itself
22:53:49 <Karen> Eric: Stick it next to part of query you want to restrict the access to
22:54:13 <Karen> Scott: So if you could get hospital IT to use access control, they can control data and should be happy
22:54:21 <Karen> ...Still it's technically possible
22:54:39 <Karen> Jeff: I did a project five years ago, people wanted to keep their data bases to themselves
22:54:46 <Karen> ...we had to do a lot of training and education
22:54:50 <Karen> ...It's a big obstacle
22:54:57 <Karen> ...Have to see what their concerns are
22:55:05 <Karen> Scott: Another tact for engineers
22:55:36 <Karen> Eric: Mechanical engineers like the explicit graph
22:55:50 <Karen> ...data model simplicity and publishing are clear
22:56:08 <Karen> Scott: Any other ideas about resources
22:56:23 <Karen> ...I am strongly in favor of grants that would take members of this HCLS community along
22:56:27 <Karen> ...and give us more resources
22:56:38 <Karen> ...Some efforts to hire Eric that way, for example
22:56:45 <Karen> ...someone from W3C who can do more of that work
22:56:50 <Karen> ...beyond membership
22:57:06 <Karen> ...I hope there are other people who can come up with grant ideas and proposals to help move things along
22:57:16 <Karen> ...One evolved out of an ELS proposal
22:57:28 <Karen> Kei: Yes, we need to pursue this
22:57:36 <Karen> ...It takes a long time
22:57:44 <Karen> ...nine months to a year
22:57:53 <Karen> ...before you get the funding
22:58:52 <Karen> Harold: What about speakers from this group?
22:59:03 <Karen> Scott: Susie, Eric and I do our best to spreak the work around
22:59:14 <Karen> ...We just visited EBI, Uniprot, BioIT
22:59:27 <Karen> ...Pharma IT, SemWeb PRISM Forum
22:59:38 <Karen> ...Everytime I talk about HCLS, there are people who are interested
22:59:44 <Karen> Harold: So we can send invites
22:59:47 <Karen> ...good to know
22:59:57 <Karen> ...So let's take a break and be on schedule
23:00:32 <Karen> Harold: Yes, and I'll do my talk when we come back
23:00:37 <Zakim> -ElgarPichler
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23:17:36 <matthias_samwald> I need to leave the call now, bye everyone!
23:17:41 <Zakim> -??P3
23:32:00 <ericP> thanks for coming matthias_samwald!
23:35:54 <andreasplendiani> andreasplendiani has joined #HCLS
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23:41:51 <ericP> Zakim, who is here?
23:41:51 <Zakim> On the phone I see HCLSf2f
23:41:52 <Zakim> On IRC I see Karen_, csma, Jeffery, andreasplendiani, masao, Karen, allen, mm, egonw, LenaDeus, RRSAgent, Zakim, matthias_samwald, Cloud, ericP
23:42:14 <Karen_> Scott: Ok, let's continue
23:42:22 <Karen_> Harold: So Semantic Wiki
23:42:33 <Karen_> ...much can be found on the ontolog site
23:42:34 <ericP> scribenic: Karen_ 
23:42:46 <Karen_> ..Focus on Semweb wiki
23:43:05 <Karen_> ...Here is BioMOBY on wikipedia
23:43:12 <Karen_> ...If it's red, it has not been created yet
23:43:36 <Karen_> ...So I can get invited in different ways
23:43:43 <Karen_> ...This is full of wonderful facts we would like to mine
23:43:50 <Karen_> ...but can only do it using some sort of MLP
23:43:51 <nigam> nigam has joined #hcls
23:43:59 <Karen_> ...Would be realy interesting to get that into triples
23:44:03 <Karen_> ...similarly
23:44:08 <Karen_> ...an entertaining problem
23:44:23 <Karen_> [looking for scroll bar, go to bottom]
23:44:35 <Karen_> ...Someone has assigned BioMOBY to a couple of categories
23:44:37 <Karen_> ...How this is done
23:44:43 <Karen_> ...Cut down HTML
23:44:50 <Karen_> ...link to something else inside
23:44:55 <Karen_> ...a registry of web services
23:44:58 <Karen_> ...which we link
23:45:07 <Karen_> ...someone put SemanticMoby in brackets
23:45:10 <Karen_> ...Go to bottom
23:45:17 <Karen_> ...and here are our the category links
23:45:22 <Karen_> ...The Semantic Wikipedia people
23:45:25 <Karen_> ...looked at this
23:45:39 <Karen_> ...and knows that BioMOBY belongs to category bioinformatics
23:45:49 <Karen_> ...They said BioMOBY is an instance
23:46:06 <Karen_> ...So we can glean the fact that Bioinformatics is a subclass of informatics
23:46:11 <Karen_> ...What's missing, to make it complete
23:46:29 <Karen_> ...Utilizes RDF
23:46:40 <Karen_> ...The verb is sitting out here
23:46:44 <Karen_> ...So we extend the syntax
23:46:53 <Karen_> ...and put your connector inside the brackets
23:46:58 <Karen_> ...now I have  triple
23:47:06 <Karen_> ...BioMOBY...Utilizes...RDF
23:47:13 <Karen_> ...that is what they did
23:47:24 <Karen_> ...the addition of this to extend media wiki into semantic media wiki
23:47:35 <Karen_> ...So once you get semantic media wiki, I can edit pages
23:47:45 <mscottm> mscottm has joined #hcls
23:49:17 <Karen_> ...So I created this property
23:49:28 <Karen_> ...Scroll down to bottom, so when you hit a property, you can find relationships
23:49:37 <Karen_> ...And building something that looks like a triple store
23:49:41 <Karen_> ...What we are fighting to correct
23:49:53 <Karen_> ...It's so close to a triple store, it's frustrating that it's not [laughs]
23:49:59 <Karen_> ...The semantic media wiki people
23:50:07 <Karen_> ...believe that the text should be the source of the information
23:50:13 <Karen_> ...and the embedded info should be the objects
23:50:17 <Karen_> ...We are working with Ontoprise
23:50:29 <Karen_> ...We want a triple store behind this that goes both directions
23:50:35 <Karen_> ...So that's coming slowly
23:50:45 <Karen_> Eric: So I do a SPARQL update that creates a new protein
23:50:46 <allen> please provide "state of interest HCLS as a pdf file
23:50:55 <Karen_> ...and go to wiki page and it's sparsely populated
23:51:02 <Karen_> ...What I wrote into triple store
23:51:07 <Karen_> ...and read from wiki side, what do I see?
23:51:11 <Karen_> ...Looking for ideas
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23:51:16 <Karen_> Harold: One thing you can do
23:51:19 <Karen_> ...is through a URL
23:51:24 <Karen_> ...but I'm doing it manually
23:51:31 <Karen_> ...I can pull what's recorded in wiki in RDF
23:51:40 <Karen_> ...You can pull stuff out in Jason
23:51:48 <Karen_> ...and use an Ajax server for other devices
23:51:52 <Karen_> ...By going to URLs
23:51:57 <Karen_> ...They have added
23:52:29 <Karen_> [Harold looking]
23:52:44 <Karen_> ...This should look familiar to people who know MIT Simile project
23:52:48 <Karen_> ...a neat way to do RDF data
23:52:59 <Karen_> ...You can select, slice and dice and organize as tables different view
23:53:02 <Karen_> ...of triple data
23:53:05 <Karen_> ...MIT did this
23:53:18 <Karen_> ...What's nice is this one has embedded a SPARQL test query
23:53:29 <Karen_> ...put in an ask and everything that has this relationship
23:53:44 <Karen_> ...with oncology lesion measurement
23:53:51 <Karen_> ...look at domain
23:53:55 <Karen_> ...look at formats
23:54:03 <Karen_> ...this is a SPARQL like query language
23:54:17 <Karen_> ...Allows you to construct pages and do fancy queries
23:54:23 <Karen_> ...Then become exportable in RDF and OWL
23:54:28 <Karen_> ...It's almost RDF
23:54:35 <Karen_> ..So almost an RDF end point 
23:54:41 <Karen_> Scott: It's Exhibit
23:54:57 <Karen_> Harold: It builds itself almost like a mini triple store
23:55:16 <Karen_> ...So we have idea of creating, querying the triples
23:55:25 <Karen_> Nagim: This does not look like semantic media wiki
23:55:30 <Karen_> ...not embedded in some container
23:55:38 <Karen_> Harold: That's what's nice about media wiki
23:55:43 <Karen_> ...If there is something you want to do
23:55:53 <Karen_> ...somebody else has probably wanted to do it, too
23:56:03 <Karen_> ...So you select which solution fits your use case best
23:56:10 <Karen_> ...This is one of hundreds of little add-ons
23:56:15 <Karen_> ...Turned out to be useful
23:56:39 <Karen_> Nagim: But what I'm saying is that it's something else
23:56:47 <Karen_> Harold: no, it's semantic media wiki
23:57:10 <Karen_> ...This is one called category tree
23:57:16 <Karen_> ...showing that we loaded SNOMED CT
23:57:20 <Karen_> ...How we use it
23:57:30 <Karen_> ...the Ontolog people have created set of extensions called HALO
23:57:36 <Karen_> ...If I'm editing
23:57:41 <Karen_> ...mentioning properties
23:57:45 <Karen_> ...You can do an inline search
23:57:49 <Karen_> ...gene is a biomarker up
23:57:53 <Karen_> ...define properties
23:57:57 <Karen_> ...this one defined by NCI
23:58:13 <Karen_> ...This is another set of tools, the auto completion