Project diagrams

[petermr]

Create a component diagram of the project , using graphvis/dotty if possible.

[petermr]

Components

articles

getpapers

dictionaries

activity

compound

plant

instrument

targetOrganism

ami

ami-search

 ami-pdf

[petermr]

see http://discuss.contentmine.org/t/overall-architecture/142 for overview. 4 years old but still more or less OK. Need more on dictionaries.

[EmanuelFaria]

Folks,

It may help get this diagram process rolling.

I’ve built a concept map in CMAP Tools (File attached as DAVEconceptMap20191003.pdf).

If there is interest, we could stick it in the CMAP cloud and contribute together. I've attached a zipped file for that too.

DAVEconceptMap20191003.pdf DAVE neural net.cmap.zip

[petermr]

Thanks Manny, This is a useful guide to some of what we are doing. It is, as you say, a concept map - things that are, or might be relevant. (The lower part of the diagram is somewhat in the future, especially for machine extraction.) It's useful for people to see the green RHS - which is not part of this project but shows its values.

@deadlyvices and I are going to produce an engineering diagram - "schema"

• which details the precise components and how they interoperate. These can probably be mapped onto some of the parts of the CMAP.

Is the CMAP software OPen? FreeToUse? we do not want to get lockin to proprietary tools and standards.

P.

On Fri, Oct 4, 2019 at 8:45 PM Emanuel Faria notifications@github.com wrote:

Folks,

It may help get this diagram process rolling.

I’ve built a concept map in CMAP Tools https://cmap.ihmc.us (File attached as DAVEconceptMap20191003.pdf). DAVEconceptMap20191003.pdf https://github.com/petermr/CEVOpen/files/3692063/DAVEconceptMap20191003.pdf DAVE neural net.cmap.zip https://github.com/petermr/CEVOpen/files/3692070/DAVE.neural.net.cmap.zip

If there is interest, we could stick it in the CMAP cloud and contribute together. I've attached a zipped file for that too.

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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[deadlyvices]

It seems to be free for academic use.

[EmanuelFaria]

Yes. CMAP is Free to use on desktop and/or in the cloud (it may also work on mobile browsers, not sure).

One of the reasons I like to use this tool is that (on Mac) I can hit command—L and automatically reorganize the map in several ways. I’m a visual thinker, so it helps me see new connections immediately that I wouldn’t otherwise. Very handy feature! Also, you can embed links to other CMAPs to dig deeper into supporting concepts without cluttering the main one. Similar purpose to hyperlinks in blog posts etc.

My intention of this map was to display my thoughts and my data desires/needs that will enable me to “micro formulate” for the different needs the skin has, beyond just, say, getting rid of an invading organism.

Also, to stimulate conversation and the possible generation of new ideas and capabilities — to plan for, if not add to this iteration.

I’ll see how to get what I’ve built into the cloud later today, just in case we’d like to play around in there. It’s as easy as clicking any concept or joining box and dragging to drop a new one with joiner complete. Love it.

_{Sent with GitHawk}

[EmanuelFaria]

It seems to be free for academic use.

@deadlyvices love the username by the way! What’s your real world name, friend?

Manny

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[deadlyvices]

Clyde Davies. I fed it into an anagram generator, and look what popped out 😁

On Sat, Oct 5, 2019 at 2:37 PM Emanuel Faria notifications@github.com wrote:

It seems to be free for academic use.

@deadlyvices https://github.com/deadlyvices love the username by the way! What’s your real world name, friend?

Manny

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-- Clyde

[EmanuelFaria]

Hi Clyde! That’s awesome! I’m going to try that

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[EmanuelFaria]

First time doing this, but looks like I was able to post my map to the cloud and send all of you emails with permission to edit and comment on it without needing to install the app.

Please have a look at "DAVE neural net" here:

https://cmapscloud.ihmc.us:443/rid=1V2BTF0TJ-LKQ4XY-1198P41

[deadlyvices]

OK, my first stab at a cloud diagram. See if you can access this: https://cmapscloud.ihmc.us/viewer/cmap/1V2DR2S7C-28741FY-97

[petermr]

Looks good to me.

Does CMAP add semantics to this? or is it primarily a graph-editor? Does it output test files (e.g. dotty)

I note the software runs on all platforms

On Sun, Oct 6, 2019 at 11:54 AM Clyde Davies notifications@github.com wrote:

OK, my first stab at a cloud diagram. See if you can access this: https://cmapscloud.ihmc.us/viewer/cmap/1V2DR2S7C-28741FY-97

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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[deadlyvices]

Not sure about the semantics. Or the dotty export. I'll investigate.

The solid arrows indicate things we do already. The dashed arrows are things we could or should do.

[deadlyvices]

It does semantics! You can export the map as a CXL file (XML) so it's simply a case of writing a little tool to generate the dotty from that.

[deadlyvices]

@mannyrules my vices are actually pretty pedestrian. Limited to the odd glass of malt and a cigar on my birthday. And ignoring the dog when he wants to go for a walk in the rain.

[deadlyvices]

Ok, I've updated the diagram. Have a look at it and see if it needs anything adding and tell me. or, better still, add it yourself!

[EmanuelFaria]

Can you share the cloud folder you've placed your map with me please? I'd like to access the map with the desktop app. please add: mannyrules@me.com or mannyrules@gmail.com

P.S. When I added everyone's emails to my cmap, I edited the preference for everyone to full editing access. But when I checked again today, I had to go back in there and reset the permissions again.

[EmanuelFaria]

It does semantics! You can export the map as a CXL file (XML) so it's simply a case of writing a little tool to generate the dotty from that.

Can someone quickly explain (or point me to an explanation of) "adding Semantics" and "dotty" please?

[deadlyvices]

OK: semantics in this context means we can extract meaningful info from the export, so instead of just a file which describes a bunch of shapes and their physical location, we can get out the logical relationships between them. This is where dotty comes in. dotty is a textual language describing a directed graph. It's simply a list of pairs of joined nodes. So a very simple tree could be described by a->b a->c And that's it. Very easy to generate if you have a semantic description to start with.

[deadlyvices]

@mannyrules I've tried setting the permissions but it doesn't seem to recognise my password. Despite resetting it. let me try again tomorrow.

[EmanuelFaria]

OK: semantics in this context means we can extract meaningful info from the export, so instead of just a file which describes a bunch of shapes and their physical location, we can get out the logical relationships between them. ...

@deadlyvices thanks Clyde :)

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[petermr]

As an example. "find all plants producing essential oils with monoterpenes from seeds of angiosperms growing in subtropical regions" You won't be able to ask google this. The papers won't use these words. But if every plant is labelled with Wikidata we know whether it's an angiosperm If every country is Wikidata-fied we know its latitude If every plantpart is Wikidatafied we know if it's a seed If the paper has semantic sections we know where to look for plant harvesting.

so we can ask these questions.

Have you used SPARQL ? That's a semantic language. Have a look at https://www.wikidata.org/wiki/Wikidata:WikiFactMine/Core_SPARQL that shows a range of examples. Some will plot maps... or timelines

On Tue, Oct 8, 2019 at 4:37 PM Emanuel Faria notifications@github.com wrote:

OK: semantics in this context means we can extract meaningful info from the export, so instead of just a file which describes a bunch of shapes and their physical location, we can get out the logical relationships between them. ...

@deadlyvices https://github.com/deadlyvices thanks Clyde :)

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[deadlyvices]

I still cannot set permissions on that graph despite changing my password. It's not the most user friendly software. I assume you can see the graph?

[EmanuelFaria]

so we can ask these questions. Have you used SPARQL ? That's a semantic language.

Thanks for the examples Peter. The technology and its uses are amazing. Too bad google doesn't have this baked in. One tweak of Google's SEO algorithm, and the world jumps. Imagine if they started scoring pages on the ease of semantic availability, or something along those lines.

[EmanuelFaria]

I still cannot set permissions on that graph despite changing my password. It's not the most user friendly software. I assume you can see the graph?

Hi Clyde, here's how you change CMAP cloud permissions (screenshots in links)...

The permission change needs to be done in the cloud.

1. The file needs to be in a folder (which you can create, and then just drag in).
2. Then, click on the folder, not the file...
3. once clicked, look to the left menu bar and click "Share".
4. If you see my email address in the top left box, select it, (If you don't see my address, add mannyrules@gmail.com [return] and mannyrules@me.com],
5. use the arrows in the middle of the window to move it to the bottom, and then select the new permission from the bottom drop-down menu and hit share.

That should do it.

If none of that works, you could send me a copy of the "Essential Oils Overview.cmap" file on your hard drive and I can put it in the cloud for us with permissions turned on.

[petermr]

On Wed, Oct 9, 2019 at 1:40 PM Emanuel Faria notifications@github.com wrote:

so we can ask these questions. Have you used SPARQL ? That's a semantic language.

Thanks for the examples Peter. The technology and its uses are amazing. Too bad google doesn't have this baked in. One tweak of Google's SEO algorithm, and the world jumps. Imagine if they started scoring pages on the ease of semantic availability, or something along those lines.

Google knows all about this and certainly has triplestores inside. They +MS+Yahoo (GYM) launched schema.org which tags many thousand items. They are working with Wikidata on this. But they don't share their data and they don't expose their triplestore API.

There's enough triplestore tech out there. We might even piggyback on Wikipedia.

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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

[deadlyvices]

Manny I think that's worked now. I was trying to set permissions from the desktop client, not the web client

Check to see if you can access it Clyde

On Wed, Oct 9, 2019 at 1:56 PM Emanuel Faria notifications@github.com wrote:

I still cannot set permissions on that graph despite changing my password. It's not the most user friendly software. I assume you can see the graph?

Hi Clyde, here's how you change CMAP cloud permissions (screenshots in links)...

The permission change needs to be done in the cloud.

1. The file needs to be in a folder (which you can create, and then just drag in).
2. Then, click on the folder https://www.dropbox.com/s/w38ngpz0p0xil4i/Screenshot%202019-10-09%2009.44.53.png?dl=0, not the file...
3. once clicked, look to the left menu bar and click "Share".
4. If you see my email address in the top left box https://www.dropbox.com/s/h5bq0jctrqqqcdi/Screenshot%202019-10-09%2009.45.46.png?dl=0, select it, (If you don't see my address, add mannyrules@gmail.com [return] and mannyrules@me.com],
5. use the arrows in the middle of the window to move it to the bottom, and then select the new permission from the bottom drop-down menu https://www.dropbox.com/s/2ch6gljxu62pr98/Screenshot%202019-10-09%2009.45.58.png?dl=0 and hit share.

That should do it.

If none of that works, you could send me a copy of the "Essential Oils Overview.cmap" file on your hard drive and I can put it in the cloud for us with permissions turned on.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/petermr/CEVOpen/issues/28?email_source=notifications&email_token=ACM3QMR7L34S4VISJID4LETQNXIGPA5CNFSM4I5OE5S2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAXZBKQ#issuecomment-539988138, or mute the thread https://github.com/notifications/unsubscribe-auth/ACM3QMTRKM2FZJLPKVLCNJLQNXIGPANCNFSM4I5OE5SQ .

-- Clyde

[deadlyvices]

Did you manage to access the graph? I shared it with you. The web client says it's locked so I assume you are currently in it.

Cheers Clyde

On Wed, Oct 9, 2019 at 1:56 PM Emanuel Faria notifications@github.com wrote:

I still cannot set permissions on that graph despite changing my password. It's not the most user friendly software. I assume you can see the graph?

Hi Clyde, here's how you change CMAP cloud permissions (screenshots in links)...

The permission change needs to be done in the cloud.

1. The file needs to be in a folder (which you can create, and then just drag in).
2. Then, click on the folder https://www.dropbox.com/s/w38ngpz0p0xil4i/Screenshot%202019-10-09%2009.44.53.png?dl=0, not the file...
3. once clicked, look to the left menu bar and click "Share".
4. If you see my email address in the top left box https://www.dropbox.com/s/h5bq0jctrqqqcdi/Screenshot%202019-10-09%2009.45.46.png?dl=0, select it, (If you don't see my address, add mannyrules@gmail.com [return] and mannyrules@me.com],
5. use the arrows in the middle of the window to move it to the bottom, and then select the new permission from the bottom drop-down menu https://www.dropbox.com/s/2ch6gljxu62pr98/Screenshot%202019-10-09%2009.45.58.png?dl=0 and hit share.

That should do it.

If none of that works, you could send me a copy of the "Essential Oils Overview.cmap" file on your hard drive and I can put it in the cloud for us with permissions turned on.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/petermr/CEVOpen/issues/28?email_source=notifications&email_token=ACM3QMR7L34S4VISJID4LETQNXIGPA5CNFSM4I5OE5S2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAXZBKQ#issuecomment-539988138, or mute the thread https://github.com/notifications/unsubscribe-auth/ACM3QMTRKM2FZJLPKVLCNJLQNXIGPANCNFSM4I5OE5SQ .

-- Clyde

[EmanuelFaria]

Got it! Thanks Clyde :)

[deadlyvices]

The solid links are things I think we do already. The dashed links are things we should probably do.