Taxonomic and database stats extracted and displayed on home page

[jsimons9]

I would like to capture the total number of interactions in the database, the total number of unique interactors (this would include non-biological and unidentified stuff), and the total number of unique biological taxa in the database and display those somewhere on the homepage near the top of the page. Also, we could include the total of references/contributors to the database.

[reedhewitt]

@jhpoelen Is there a way to get those numbers programmatically so that I can access them through a REST interface? JSON or even a plain number would work. If you have a way to make those numbers available, I can take care of inserting them on the home page.

[reedhewitt]

@jsimons9 I think I have all the information I need from Jorrit to add these stats to the home page. The only thing I'm not sure about is "unique interactors". Can you describe what that means?

[jsimons9]

Hi Reed,

OK, the total unique interactors is merely a list of all unique items that have been either predator or prey, including non-biological taxa such as detritus, or sand, or plastic, etc. Then there is a unique taxa which is only biological taxa.

The total number of interactions should be the largest number, then the unique interactors and finally the biological taxa should be the smaller of the three numbers.

Hope this helps.

Jim

From: Reed Hewitt [mailto:notifications@github.com] Sent: Thursday, October 10, 2013 8:38 AM To: jhpoelen/gomexsi Cc: Simons, James Subject: Re: [gomexsi] Taxonomic and database stats extracted and displayed on home page (#78)

@jsimons9https://github.com/jsimons9 I think I have all the information I need from Jorrit to add these stats to the home page. The only thing I'm not sure about is "unique interactors". Can you describe what that means?

— Reply to this email directly or view it on GitHubhttps://github.com/jhpoelen/gomexsi/issues/78#issuecomment-26054084.

[jhpoelen]

@reedhewitt please see example on http://eol-globi.github.io for an example of how to use the study stats.

[reedhewitt]

Thanks. I was just working on the statistics display for the home page today. I should have it up tomorrow.

[reedhewitt]

@jsimons9 The following statistics are now displayed on the GoMexSI home page:

• Number of contributing studies
• Number of visits since the launch of the site
• Number of predators
• Number of prey
• Total number of interactions

They are in that order because that puts the numbers in ascending order, which just looked right to me. The numbers are fetched after the page loads, so that the page itself is not hung up while waiting for the data. Once the statistics are retrieved, I have the numbers animated to "count" up from zero to the full value, which looks cool and draws attention to the numbers.

Those statistics are inserted using the shortcode [stats], so they can be moved anywhere on the home page or even placed on other pages. Let me know what you think!

[jsimons9]

Reed,

One thing I discovered when speaking with Jorrit yesterday is that those numbers include GloBI records too, so we probably should not display that until we have worked out the filtering of those numbers.

Jim

From: Reed Hewitt [mailto:notifications@github.com] Sent: Friday, November 01, 2013 5:09 PM To: jhpoelen/gomexsi Cc: Simons, James Subject: Re: [gomexsi] Taxonomic and database stats extracted and displayed on home page (#78)

@jsimons9https://github.com/jsimons9 The following statistics are now displayed on the GoMexSI home page:

• Number of contributing studies
• Number of visits since the launch of the site
• Number of predators
• Number of prey
• Total number of interactions

They are in that order because that puts the numbers in ascending order, which just looked right to me. The numbers are fetched after the page loads, so that the page itself is not hung up while waiting for the data. Once the statistics are retrieved, I have the numbers animated to "count" up from zero to the full value, which looks cool and draws attention to the numbers.

Those statistics are inserted using the shortcode [stats], so they can be moved anywhere on the home page or even placed on other pages. Let me know what you think!

— Reply to this email directly or view it on GitHubhttps://github.com/jhpoelen/gomexsi/issues/78#issuecomment-27604956.

[reedhewitt]

No problem. I removed the shortcode for the time being, so the stats are not on the home page right now.

[jhpoelen]

I've just extended the GloBI REST api to include ability to only include studies that came from gomexsi. The functionality should be available by tomorrow morning.

@reedhewitt see https://github.com/jhpoelen/eol-globi-data/wiki/Rest#references-to-datasets . The idea is to get the source you'd like from the sources list. Then do info / contributor query for particular source.

PS I've been working on this javascript api and I was wondering whether we should used it in GoMexSI. . . see https://npmjs.org/package/globi-data . Curious what you think . . .

[reedhewitt]

@jhpoelen I'm getting 404 errors with the /info and /contributors links. Can you see if it's working for you?

That Javascript API looks like a great tool. That may be handy for future developments and feature additions to GoMexSI.

[jhpoelen]

Thanks for sharing this. I was able to reproduce and will look at this as soon as I can.

thx, -jorrit

[jsimons9]

Hi Reed,

I have some proposed changes to the categories.

How about changing the first one to: Number of references/contributors

Drop the second from this display. I was thinking this and the number of registered users (if we use these at all) could go somewhere else.

Combine Predators and Prey into: Number of unique interactors This would include an interactor at any taxonomic level, but I would like to remove inanimate objects, i.e. sand, plastic, etc, but they could be included if it was too difficult to remove them (Note: Once we add parasites and other interactors this will become unwieldy as we would have multiple different categories. I would like to stick with the generic “interactors”. We could somewhere on the summary page provide a detailed break out for all groups.)

The last one is fine as is.

Comments.

Jim

From: Reed Hewitt [mailto:notifications@github.com] Sent: Friday, November 01, 2013 5:09 PM To: jhpoelen/gomexsi Cc: Simons, James Subject: Re: [gomexsi] Taxonomic and database stats extracted and displayed on home page (#78)

@jsimons9https://github.com/jsimons9 The following statistics are now displayed on the GoMexSI home page:

• Number of contributing studies
• Number of visits since the launch of the site
• Number of predators
• Number of prey
• Total number of interactions

They are in that order because that puts the numbers in ascending order, which just looked right to me. The numbers are fetched after the page loads, so that the page itself is not hung up while waiting for the data. Once the statistics are retrieved, I have the numbers animated to "count" up from zero to the full value, which looks cool and draws attention to the numbers.

Those statistics are inserted using the shortcode [stats], so they can be moved anywhere on the home page or even placed on other pages. Let me know what you think!

— Reply to this email directly or view it on GitHubhttps://github.com/jhpoelen/gomexsi/issues/78#issuecomment-27604956.

[reedhewitt]

Jim,

I'll make the changes you suggested, so we'll have three stats instead of five. (That will allow the numbers to be larger, which I think will look nice.)

Once Jorrit has the GoMexSI-specific data available, I'll publish the updated statistics block on the home page.

Reed

[jsimons9]

OK, sounds good. Not sure how big the numbers were before, but don’t make them too large or overwhelming – but then you are the design expert!!! ☺

Thanks,

Jim

From: Reed Hewitt [mailto:notifications@github.com] Sent: Monday, November 04, 2013 11:35 AM To: jhpoelen/gomexsi Cc: Simons, James Subject: Re: [gomexsi] Taxonomic and database stats extracted and displayed on home page (#78)

Jim,

I'll make the changes you suggested, so we'll have three stats instead of five. (That will allow the numbers to be larger, which I think will look nice.)

Once Jorrit has the GoMexSI-specific data available, I'll publish the updated statistics block on the home page.

Reed

— Reply to this email directly or view it on GitHubhttps://github.com/jhpoelen/gomexsi/issues/78#issuecomment-27705123.

[reedhewitt]

I'll keep them to a reasonable size. : )

[jhpoelen]

@reedhewitt thanks again for reporting the issue - I've made a minor change to the GloBI API, using request (query) parameters instead of path. See https://github.com/jhpoelen/eol-globi-data/wiki/rest#references-to-datasets for info. The changes should be available by tomorrow afternoon, in the next iteration of generating the GloBI data. Please feel free to re-open the issue if you can't get to the information you'd like.

[jhpoelen]

re-open: I'll let Jim close the issue once the UI is active.

[reedhewitt]

@jhpoelen Thanks for the update. I'll check the API this afternoon and make the changes to the stats shortcode.

[jhpoelen]

Hi Reed,

Just confirmed that the changed had not been applied.

I’ve updated the API manually and the urls seem to be working now. Please confirm.

thx, -jorrit

PS http://trophicgraph.com:8080/contributors?source=SPIRE yields:

{ "columns" : [ "study.institution?", "study.period?", "study.description", "study.contributor", "count(interact)", "count(distinct(sourceTaxon))", "count(distinct(targetTaxon))", "study.title" ], "data" : [ [ null, null, "Christian RR, Luczkovich JJ (1999) Organizing and understanding a winter's seagrass foodweb network through effective trophic levels. Ecol Model 117:99-124", "", 270, 82, 85, "Christian RR, Luczkov...a17608f43ca269eea90bec6715802d26" ], [ null, null, "R. D. Bird, Biotic communities of the Aspen Parkland of central Canada, Ecology, 11:356-442, from p. 393 (1930).", "", 14, 9, 9, "Bird, Biotic communit...bf87784bd826c93b133eb9f9403563d1" ], [ null, null, "B. C. Patten and J. T. Finn, Systems approach to continental shelf ecosystems. In: Theoretical Systems Ecology, E. Halfon, Ed. (Academic Press, New York, 1979) pp. 183-212 from p. 202.", "", 21, 7, 9, "Patten and Finn, Syst...8fb5b624c2ee17545c06b8270f0c6f3b" ], [ null, null, "G. W. Minshall, Role of allochthonous detritus in the trophic structure of a woodland springbrook community, Ecology 48(1):139-149, from p. 148 (1967).", "", 36, 14, 10, "Minshall, Role of all...1807c189e1f1ff38acf1cccae5c23a1a" ], [ null, null, "L. Saldanha, Estudio Ambiental do Estuario do Tejo, Publ. no. 5(4) (CNA/Tejo, Lisbon, 1980).", "", 73, 25, 23, "Saldanha, Estudio Amb...c122b6248eeeb6108aaaac5deadd8e74" ], [ null, null, "Polis GA (1991) Complex desert food webs: an empirical critique of food web theory. Am Nat 138:123-155", "", 63, 12, 11, "Polis GA (1991) Compl...e1b2870afe5f07cf1d61299146707a97" ], [ null, null, "M. R. Landry, A review of important concepts in the trophic organization of pelagic ecosystems, Helgolander wiss. Meeresunters. 30:8-17, from p. 12 (1977).", "", 15, 5, 8, "Landry, A review of i...e13f9b4824a43be1044f2b8c3048409f" ], [ null, null, "Thompson, RM and Townsend CR. 2005. Energy availability, spatial heterogeneity and ecosystem size predictfood-web structure in streams. OIKOS 108: 137-148.", "", 1217, 149, 158, "Thompson, RM and Town...635b4182bd163966ec06402f0b9f8ca8" ], [ null, null, "Y. I. Sorokin, Biological productivity of the Rybinsk reservoir. In: Productivity Problems of Freshwaters, Z. Kajak and A. Hillbricht-Ilkowska, Eds. (Polish Scientific, Warsaw, 1972), pp. 493-503, from p. 497.", "", 32, 9, 11, "Sorokin, Biological p...374f091c09ff40ac42eac32bc02512c7" ], [ null, null, "R. W. Dexter, The marine communities of a tidal inlet at Cape Ann, Massachusetts: a study in bio-ecology, Ecol. Monogr. 17:263-294, from p. 272 (1947).", "", 46, 21, 21, "Dexter, The marine co...a68479f7f2e18558c690d9c24ceb302e" ], [ null, null, "R. W. Dexter, The marine communities of a tidal inlet at Cape Ann, Massachusetts: a study in bio-ecology, Ecol. Monogr. 17:263-294, from p. 288 (1947).", "", 12, 7, 8, "Dexter, The marine co...272bb4f81cb3e8857c800e2b7c483578" ], [ null, null, "B. Corker, 1984. The ecology of the pitcher plant, Nepenthes mirabilis, andits associated fauna in Hong Kong. Ph.D. thesis, University of Hong Kong. Prior number: K. Schoenly and R. A. Beaver (1988) 3", "", 14, 8, 7, "Corker, 198 The ecolo...ec603e301a24124614c299dc627d9706" ], [ null, null, "G. E. Walsh, An ecological study of a Hawaiian mangrove swamp. In: Estuaries, G. H. Lauff, Ed. (AAAS Publication 83, Washington, DC, 1967), pp. 420-431, from p. 429.", "", 38, 14, 13, "Walsh, An ecological ...6b15aaafefe8a77c45a3bba99e73eac1" ], [ null, null, "R. R. Askew, 1961. On the biology of the inhabitants of oak galls of Cynipidae (Hymenoptera) in Britain. Trans. Soc. Brit. Entomol. 14:237-268, from p. 239-42 (after S. Pimm, 1982. Food Webs. 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[reedhewitt]

I have updated the [stats] shortcode to use only the GoMexSI data and I also changed the visible statistics to be References/Contributors, Unique Interactors, and Total Interactions.

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