globalbioticinteractions/globalbioticinteractions.github.io

source files for GloBI website

globalbioticinteractions.github.io

This project contains live examples of how to use species interaction data from GloBI (see http://github.com/globalbioticinteractions/globalbioticinteractions) in a webpage.

Live examples are available at http://www.globalbioticinteractions.org .

This website is (partly) built using npm, browserify and associated tools.

installing

npm install -g watcherify
npm install -g browserify
npm install -g uglify-js

building

npm install
npm run build

testing

npm test
npm run test-browser

developing

To continuously build the browserified (./static/globi-web-min.js) run:

npm run watch

globalbioticinteractions.github.io's Issues

suggest to include ability to search by source, interaction types and target

as discussed with @jhammock and Michele Weber @mxweber :

Suggest to include a way to specify source , target and interaction type to restrict interactions of interest.

Included a rough sketch of one (of the many) ways to provide this functionality. Note the proposed purple search fields on top of the columns.

globi-search tests are failing (and not executing on travis)

Hi @coding46 - I was working on globi-search module and noticed that the TypeSelector test (since renamed to test/addRemoveOptions.js failed due to (what I believe is) a DOM timing issue. Unfortunately, travis is not picking up the tests because it doesn't seem to install globi-search properly in the pre-install phase.

Let me know if you can reproduce the test failures. If so, please fix them.

reintroduce study links (urls/dois) on reference pages

create a suggestion list during typing for the source / target taxa of interest

using
http://trophicgraph.com:8080/findCloseMatchesForTaxon/Homo

travis build error due to: Cannot find module '../globi-search/lib/Mediator.js'

see https://travis-ci.org/globalbioticinteractions/globalbioticinteractions.github.io/builds/75842855 .

Was not able to reproduce on mac os. Needs more investigation.

visually highlight selected nodes and interactions in hairball

@mxweber suggested to visually highlight or bring forward the selected node and its connections in the hairball. This is to better see the local web of that specific node.

Perhaps we can do this by decreasing the alpha levels of non-selected nodes, links and names.

create bipartite graph using spatial search parameter and/or src/target taxon search params

render the bipartite graph using the parameters provided with item from issue #1 and #2 .

suggestion for real-time database tracker

It was great to see Jorrit's presentation at UC Berkeley on Thursday. I am writing to follow up on the discussion and to suggest adding a feature that would allow users to see how many contributing databases are active at the moment of data search or download. This could be helpful in situations when major contributing databases are offline or in temporary maintenance. Their temporary absence from the pool of linked sources would result in potentially incomplete information for the user and depending on what the user needs, they may decide to check for a more comprehensive dataset later. Perhaps it could be something very simple like a counter showing the number of active databases relative to the number of total potentially available, possibly with the names of active databases (just for major databases, not individual pieces of information that may also change in time). Thanks again! Iryna

provide more info / context for taxa in interactions browser

as discussed with @jhammock and Michele Weber @mxweber :

Currently, the browser pages contains scientific names of taxa involved in interactions. To further inform users about the nature of the taxon, more information would be helpful.

One way to do this could be to show an info box appears when hovering / clicking on taxon name wherever one appears on the page. The info box would contains a thumbnail, scientific name, common name (if available) and link to EOL taxon page (or other when available).

add record count to the tabular interaction view in the interaction browser

As discussed with @jhammock and Michele Weber @mxweber .

Currently, the tabular search results include source/ target taxon and interaction type. Suggested to include a count of the number of records available for this interaction as a forth column. The idea is to provide the user with a way of seeing how much data is available for a specific interactions.

spatial queries slow on browse page

When selecting a point or area on the map in the browse page, the queries take a long time > 10s to return. It would be nice to make it a little more snappier. Particularly when using higher order taxa like Animalia or Aves. Suspect that some "smarter" pagination might work (on the server side).

add higher taxon order icon to species interaction browser

as discussed with @jhammock and Michele Weber @mxweber:

Currently, scientific names are used to indicate interacting taxa in the interaction browser. To give an indication of the kind of taxa (e.g. birds, insects, mammals), icons are used, similar to what iNaturalist is using (see screenshot taken from http://www.inaturalist.org/taxa/7079-Oxyura-jamaicensis).

@pleary @kueda would it be ok if we recycle / re-use the pretty iconic taxa you use on iNaturalist https://github.com/inaturalist/inaturalist/tree/master/app/assets/images/iconic_taxa ? If so, how can we best attribute iNat for this?

ensure that widget allows for non-geolocated interaction data

as discussed with @jhammock .

allow taxonomic interaction search without spatial constraits

currently you have to select a region before being able to do a spatial taxonomic search

During review meeting @KatjaSchulz @mariestuder @jhammock and @mxweber suggested to allow for interaction searches without any spatial constraints.

interaction type infobox on mouse over / click in interaction browser

as discussed with @jhammock and Michele Weber @mxweber :

To inform users with the definition of an interaction types (preys on, parasite of), an info box pops up on mouse over / mouse click. This info box contains a short description and link to definition in the relation ontology.

create a list view of the interactions based on the spatial and taxonomic search parameters

this list view answers the question:

who eats what?

suggest to move taxon search upper left, map to upper right

as suggested during review session to support #37

change result list headers

currently the result list headers look like:

@mariestuder suggested to change to something like:

taxon                    interacts with                       taxon
(136 distinct)         (3711 interactions)              (379 distinct)

where the middle column reflects the currently selected interaction type

add margin to bundle view to ensure that content fits in box

@jhammock suggested to add some more margin in the bundle view, so that the circle better fits in the (maximized) panel.

suggest to include a network diagram ("hairball") visualization in interaction browser

as discussed with @jhammock and Michele Weber @mxweber :

To help provide different views on the complex interaction data in the interaction browser, suggest to include a graph visualization using balls and sticks in addition to the circular interaction plots. The underlying idea is to show the interaction data in three ways: a force-directed network diagram in addition to the existing tabular view (top left), a dependency wheel (bottom right).

An example can be found: http://fieldguides.eol.org/eco/ecovis.php?ecosystem=39#

taxon selector uses initial spatial selection only

To reproduce:

1. select a spatial area
2. click on "show interactions" to update the visualizations
3. enter a search clause in the taxon selector
4. change spatial area, click on "show interactions"
5. enter same search clause in taxon selector

expected result:
the taxon selector results are different, because of the change in spatial selection.

actual result:
taxon selector result is same - appears that the spatial search parameter are not applied to the taxonomic interaction search widget.

[FEATURE] Connect visualisations with search widget

If one clicks on a taxon node in dependency wheel / bundle view ... this selection should trigger a new search with this taxon and the most general interaction type.

switch taxonomic search suggestion in search widget to use the api

Currently, the search widget is using the observation data to suggest names.

To simply the name lookup, suggest to use the methods available through the api http://api.globalbioticinteractions.org/findCloseMatchesForTaxon/Mencsh .

@coding46 I've updated API to use the name fields / selectors just like those used in interaction queries.

suggest to apply iNaturalist taxon color scheme to indicate taxonomic context

To help identify taxa, @KatjaSchulz et al. suggested to apply iNaturalist color schemes in the GloBI pages.

describe purpose of interaction browser panels in text

@mariestuder suggested to include a description for each of the widgets used in the interaction browser (particularly the bundle/ hairball visualizations) to help the user understand their purpose.

on hiding spatial selection, spatial contraints are still applied

Steps to reproduce:

1. go to browser: http://globalbioticinteractions.org/browse
2. list human pathogens by select a taxon of interest (e.g. Homo sapiens) an interaction type (e.g. has pathogen)
3. after the results have rendered, select a spatial area
4. (currently no pathogen information exist with spatial info) after seeing an empty result set, disable or hide the spatial selector
5. re-trigger the search

currently:
an empty result re-appears - it seems that the spatial constraints are still applied, even though they are hidding

expected:
non-empty results - on hiding the spatial selector, all interactions should be shown

order interaction list: first show georeferenced ones

As suggested by @KatjaSchulz - in list show georeferenced interactions first, then those without: interaction with coordinates are typically of higher quality and more interesting

include link in interaction widget to download interaction data

suggested by @KatjaSchulz :

After getting a result in the taxon search widget, a download button should be available to retrieve all observations / interaction records associated with the results.

For instance, a search for birds (Aves) eating insects (Insecta) as a specific location would have a download button pointing to:

http://api.globalbioticinteractions.org/interaction.csv?sourceTaxon=Aves&targetTaxon=Insecta&interactionType=preysOn&type=csv&includeObservations=true&bbox=-125.53344800000002,32.750323,-114.74487299999998,41.574361&field=source_taxon_name&field=source_taxon_external_id&source_taxon_path&field=interaction_type&field=target_taxon_name&field=target_taxon_external_id&field=target_taxon_path&field=latitude&field=longitude&field=study_citation&field=study_url&field=study_source_citation

include number of distinct source and target taxa in interaction widget result

as suggested by @katjaschultz :

When showing search results, include the number of distinct source and target taxa in the search results to inform the user on the richness of the results. Something along the lines of: 35 birds (Aves) taxa found and 54 insects (Insecta) taxa found.

hard and unclear to discover interaction data on Moorea using browse tool

Today, Neil Davies tried to use the browse tool at http://globalbioticinteractions.org/browse . The process appeared to be slow and it was unclear how to relate the interaction to the data source.

Steps involved were:

1. Searched for Moorea on map

2. Found one record on Moorea

3. Downloaded csv (took >5mins) - attached

4. Searched for
   EOL:588060 on EOL

5. found source http://eol.org/data_objects/23998215

6. searched Discover Life for 588060 and found http://www.discoverlife.org/mp/20l?id=CSCA_TCN00011460

map recenters on California when enabling the area picker on browse page

When showing the area picker in http://globalbioticinteractions.org/browse/ page, I find it hard to locate or change the area picker.

use case:

1. zoom in on Carribean
2. select area or interest

expected:
When selecting an area of interest a rectangle is shown within the shown map. The position and size of rectangle can then be changed using touch / mouse events.

actual:
When selecting the "show area picker", the map jumps to California. To select some area in the Carribean, the area needs to be dragged from California to the Carribean (see attached first two images).

suggestion:
A leafletjs.org plugin at https://github.com/heyman/leaflet-areaselect/ uses an approach that always centers the area selector in the middle of the map. To change position, the area selector stays fixed, and the map moves underneath it. For an example (within marker clustering) see http://globalbioticinteractions.org/browse/map (see last images).

update hairball and bundle diagram when new search parameters are entered

Whenever spatial, taxonomic or interaction type parameters are updated, all related views of the interaction data should be updated accordingly.

add placeholder image for species w/o image

As discussed last week: Not all taxa have images associated to them, and currently this shows up as a broken image link. Suggest to place an empty image (or any html element) or placeholder image whenever image is not available.

when searching for Amphibia, two Amphibia suggestions appear where one “works better” than the other.

As observed by @jhammock review meeting:

when searching for Amphibia, two Amphibia suggestions appear where one “works better” than the other.

Request for interaction data dies with a 500 Connection reset

Example:
http://trophicgraph.com:8080/interaction?nw_lat=29.3&nw_lng=-97.0&se_lat=26.3&se_lng=96.1

allow to toggle spatial constraints from list view

Currently, you have to use the selector in the map to enable/ disable spatial constraints.

@jhammock suggested to have a "show all" button in the result list to easily toggle the spatial constraint.

[BUG] Hairball breaks if result set is empty

Hairball diagramm doesn't get rendered and "blocks" rendering of bundle / update of search result list if there is an empty search response.

Breaks with a d3 error message.

workflow - suggest to start with taxon / interaction search first, then constrain geographically.

currently, a spatial selection has to be made first, then taxonomic constraints are imposed.

Michelle @mxweber suggested to optimize the tool for first selecting the taxonomic / interaction constraints, then further constrain by geographic region.

add infobox whenever a taxon node is selected

@mariestuder suggested to add a taxon info box in bundle/ hair visualization whenever a taxon node is hovered over / selected. This is to provide some taxonomic context of the node.

rough sketch:

queries repeated over and over - causing delayed response times

I noticed that the name lookup on http://globalbioticinteractions.org became unresponsive at around 12:50 Pacific time. On closer inspection, I noticed that neo4j instance was overloaded with requests. It turns out that requests are repeated over and over (see attached log).

@coding46 could this be related to recent changes you made to the interaction browser?

snippet from log (note that time stamps are in central European time.

2015-08-23 21:50:10,517 [qtp558638686-557] INFO : [...] SKIP 292864 LIMIT 1024] with params [{}]
2015-08-23 21:50:20,736 [qtp558638686-588] INFO : [...] as interaction_type SKIP 292864 LIMIT 1024] with params [{}]
2015-08-23 21:50:43,484 [qtp558638686-593] INFO : [...] SKIP 292864 LIMIT 1024] with params [{}]
2015-08-23 21:50:52,441 [qtp558638686-602] INFO : [...] SKIP 292864 LIMIT 1024] with params [{}]
2015-08-23 21:51:14,532 [qtp558638686-555] INFO :[...] SKIP 292864 LIMIT 1024] with params [{}]
2015-08-23 21:51:24,677 [qtp558638686-604] INFO : [...] SKIP 293888 LIMIT 1024] with params [{}]
2015-08-23 21:51:29,792 [qtp558638686-600] INFO : [...] SKIP 293888 LIMIT 1024] with params [{}]
2015-08-23 21:51:56,435 [qtp558638686-609] INFO : [...] SKIP 293888 LIMIT 1024] with params [{}]

use stable urls with anchors for browse page

Suggest to use scheme discussed in #16 in the http://globalbioticinteractions.org/browse pages to make it easy to share a specific state of the browser with others. The "#" style url should be updated whenever spatial or taxonomic search parameters change.

Currently, this is also possible using the "share" functionality, however, a "?" is used in the URL, causing the page to reload when used.

Current:
http://www.globalbioticinteractions.org/browse/?&bbox=-125.53344800000002,32.750323,-114.74487299999998,41.574361

Suggest to change to:
http://www.globalbioticinteractions.org/browse/#&bbox=-125.53344800000002,32.750323,-114.74487299999998,41.574361

add life stage, physiological state, body part in as fields in csv download

implement spatial search page

inspired by current: http://trophicgraph.com

1. have a way to specify the search area
2. show the locations at which information is available

NullPointerException / 500 error

http://api.globalbioticinteractions.org/interaction?type=dot&lng=-124.15033&lat=43.79654&includeObservations=true&field=source_taxon_path&field=source_taxon_path_ids&field=interaction_type&field=target_taxon_path&field=target_taxon_path_ids&field=study_citation&field=study_source_citation

I'm not sure exactly how I arrived here: I was somewhere near Fresno, and I selected "show interactions"

stable URLs

When I search for an interaction I expect a URL for the results that I can share, maybe something like http://www.globalbioticinteractions.org/#taxon=Patiria+miniata&interaction=preys_on

Problem about filtering specific species in GitHub browse

Hi, Dear editer:

Thanks so much for sharing the powerful globi browse,This is Dupont, I am having a workshop instructed by @jhpoelen at Texas A&M University, Corpus Christi , however I found myself difficult to filter the interaction linked by a single species I am interested in, (King mackerel，Scomberomorus cavalla) at http://www.globalbioticinteractions.org/browse/ in the Gulf of Mexico;

So, I am wondering if you can improve a little bit about the filtering function, Thanks.

Appreciate for your help,
Dupont

use globi-data-js for retrieving contributors list

globi-search tests not executing on travis

see #31 for related issue.

It seems that globi-search module is not being installed properly on travis for some reason. After several attempts to fix the issue, I decided to write this issue so that we don't forget.

The install files on the preinstall phase:
(see https://travis-ci.org/globalbioticinteractions/globalbioticinteractions.github.io/builds/75522883 ).

> npm cache clean & npm install ./node_modules/globi-*
untar error /home/travis/.npm/globi-search/0.0.2/package.tgz

set "interactsWith" as default interaction type

As suggested by @KatjaSchulz .

found unexpected disconnected node in interaction hairball

A disconnected node appeared in a hairball interaction diagram. E.g. Coastal giant salamander (Dicamptodon tenebrosus) somewhere in California.

Expected that all nodes are connected to at least one other node.