I recently found this ontology suite:
https://bioportal.bioontology.org/ontologies/AFO/?p=summary
I want to explore its contents. Normally I use http://www.visualdataweb.de/webvowl/ for such purposes. Example (Basic Formal Ontology):
http://www.visualdataweb.de/webvowl/#iri=http://purl.obolibrary.org/obo/bfo.owl
However, I was not able to find the IRI for the AFO ontology or at least some URL which produces a visualization at the webvowl service.
Question: How to visualize the contet of AFO?
You can try to have a look at it on the Ontology Lookup Service (OLS)
Full disclosure : I am responsible for OLS, but not AFO.
Related
I am developing an ePub. In the content.opf file I have to specify a series of metadata by using DC standard. For example dc:title and dc:creator.
However my book is a multilanguage book, that is, it contains two translations of the same text: English and Russian. The standard reference manual states that I can have more dc:language statements. For example:
<dc:language>en</dc:language>
<dc:language>ru</dc:language>
but it does not say how to specify the other metadata for more than one language. Consider, for example, dc:creator. I tried
<dc:creator xml:lang="en">Dario de Judicibus</dc:creator>
<dc:creator xml:lang="ru">Дарио де Юдицибус</dc:creator>
I get an error from the distribution platform validator, which states that the format of ePub is not correct. It looks like I cannot use xml:lang in dc:creator even if, in theory, that is an XML attribute that can be used with any XML tag. Same for dc:title:
<dc:title xml:lang="en">My Book Title</dc:title>
<dc:title xml:lang="ru">Название Mоей Kниги</dc:title>
Could someone who has had to face the same problem as me, namely writing the OPF for an ePub that contains a text in multiple languages, tell me what is the correct way to do it? In the standards for the OPF 3.x I have not been able to find any useful information to establish this.
SOLVED
I verified my code with one of the author of the W3C specifications for OPF and he told me that what I wrote is correct, but that some validator is not used to multi-language documents, so that the problem is the validator, not the code. I write this in case someone else may have the same problem.
I use Python for plotting geospatial data on maps.
For certain map-styles, such as ["basic", "streets", "outdoors", "light", "dark", "satellite", "satellite-streets"], I need a mapbox-access token and for some geospatial plotting packages like folium I even need to create my own link for retrieving the map-tiles.
So far, it worked great with the style "satellite":
mapbox_style = "satellite"
mapbox_access_token = "....blabla"
request_link = f"https://api.mapbox.com/v4/mapbox.{mapbox_style}/{{z}}/{{x}}/{{y}}#2x.jpg90?access_token={mapbox_access_token}"
However, when choosing "satellite-streets" as mapbox-tile-ID, the output doesn't show a background map anymore. It fails with inserting "satellite-streets", "satellitestreets" and "satellite_streets" into the aforementioned link-string.
Why is that and how can I come to know what's the correct tile-ID-name for "satellite-streets"?
I found an answer when reaching out to the customer support.
Apparently, one has to access the static APIs which have specific names listed on their website:
"In general, the styles that you mentioned including
"satellite_streets" that you are referencing are our classic styles
that are going to be deprecated starting June 1st. I would recommend
using our modern static API the equivalent modern styles. This
will allow you to see the most updated street data as well.
Like the example request below:
https://api.mapbox.com/styles/v1/mapbox/satellite-streets-v11/tiles/1/1/0?access_token={your_token}
Here is more info on the deprecation of the classic styles and
the migration guide for them."
My personal adaptation after having tried everything out myself, is:
Via combining the above-mentioned with the details on how to construct a Mapbox-request link on this documention from mapbox' website,
I finally managed to make it work.
An example request looks like so (in python using f-strings):
mapbox_tile_URL = f"https://api.mapbox.com/styles/v1/mapbox/{tileset_ID_str}/tiles/{tilesize_pixels}/{{z}}/{{x}}/{{y}}#2x?access_token={mapbox_access_token}"
The tileset_ID_str could be e.g. "satellite-streets-v11" which can be seen at the following link containing valid static maps.
I want to make a network graph which shows the distribution of our documents in our folder structure.
I have the nodefile, edgefile and gephi graph file in this location:
https://1drv.ms/f/s!AuVfRBdVHkO7hgs5K9r9f7jBBAUH
What I do is:
Run the algorithm ForceAtlas2 with scaling 10-20, dissuade hub marked and prevent overlap marked, all other standard setting.
What I get is a graph with groups radial/spherical distributed. However, what I want is a tree directed network graph.
Anyone know how I can adjust Gephi to make this?
Thanks!
I just found a solution.
I tested the file format as shown on the Yed site "import excel file" page
http://yed.yworks.com/support/manual/import_excel.html
This gave me the Yed import dialog (took a life time to figure out that it's a pop up menu and not selectable through the standard menu)
Anyway, it worked and I've adjusted the test files with the data prepared for the Gehpi. This was pretty easy, I could used the source target ID's etc. Just copy paste.
I load it into Yed and used some directed and radial clustering algorithms on it. Works fine!
Below you can find the excel node/edge file used to import in Yed and the graph file you can open with Yed to see the final radial result.
https://1drv.ms/f/s!AuVfRBdVHkO7hg6DExK_eVkm5_mR
Only thing to figure out is how to combine the weight (which represents the number of documents) with the node size.
Unfortunately, as of version 0.9.0, Gephi no longer supports hierarchical graphs. Maybe try using a previous version?
Other alternatives involve more complex software, such as Graphviz, but you need a .dot file instead of your .csv. I looked all over, but could not find an easy-to-use csv to dot converter.
You could try looking at d3-hierarchy, a node.js program, but then again you need to use the not-so-user-friendly npm. If you look at the link, it looks like it can produce the kind of diagram you're looking for.
I'm using Fluent library to fire a request to Natural Language Classifier service so as to 'train' the data.
Documentation says following parameters to be passed:
name=training_data; type=file; description=training data
name=training_meta_data; type=file; description=meta data to identify language etc
Below is my code sample:
File trainingCSVFile = new File("path to training file");
Request request=Request.Post(<bluemix service url>).
bodyFile(trainingCSVFile, ContentType.TEXT_PLAIN).
bodyString("{\"language\":\"en\",\"name\":\"PaymentDataClassifier\"}", ContentType.APPLICATION_JSON);
How ever am getting internal server error which plausibly due to my request format. Can any one help me how to pass the above mentioned parameters using Fluent library on priority?
I'm going to assume that you are using Java and suggest you to use the Java SDK. You can find examples to use not only Natural language Classifier but all the Watson services + Alchemy services.
Installation
Download the jar
or use Maven
<dependency>
<groupId>com.ibm.watson.developer_cloud</groupId>
<artifactId>java-sdk</artifactId>
<version>2.10.0</version>
</dependency>
or use Gradle
'com.ibm.watson.developer_cloud:java-sdk:2.10.0'
The code snippet to create a classifier is:
NaturalLanguageClassifier service = new NaturalLanguageClassifier();
service.setUsernameAndPassword("<username>", "<password>");
File trainingData = new File("/path/to/csv/file.csv");
Classifier classifier = service.createClassifier("PaymentDataClassifier", "en", trainingData);
System.out.println(classifier);
The training duration will depend on your data but once it's trained you can do:
Classification classification = service.classify(classifier.getId(), "Is it sunny?");
System.out.println(classification);
Feel free to open an issue in the GitHub repo if you have problems
So new to MarkLogic am stuck and not finding the documentation of use. I know what i need to do, just do not know how to do it.
I have a keyvalue? search on my REST server which returns ML's standard search results and XML snippet. I want to create my own custom search result which will output a title element for my XML files.
I am aware that i need to create an XSLT transformation document and upload that to the server but do not know how to target ML's search function or how to write this out.
I have basic knowledge of XSLT, if i just created something that targets each files title using xPath will this work, or does ML require use of their custom functions?
I know its a bit broad, but hopefully someone can point steer me.
Sounds like you are talking about the GET /v1/keyvalue endpoint of MarkLogic REST API. Unfortunately that does not allow you to choose a transform. You can probably use GET /v1/search with a transform param instead though, using a structured query for an element value query. The docs contain a good syntax reference on that.
Docs on creating and managing transforms can be found here:
http://docs.marklogic.com/guide/rest-dev/transforms#chapter
HTH!
You can use extract-metadata in your search options with search:search or the /v1/search/ REST API endpoint to include the title element in a metadata element or JSON property in your results:
import module namespace search = "http://marklogic.com/appservices/search"
at "/MarkLogic/appservices/search/search.xqy";
search:search(
"my query string",
<options xmlns="http://marklogic.com/appservices/search">
<extract-metadata>
<qname elem-ns="" elem-name="title"/>
</extract-metadata>
</options>)
If you need more flexibility, you specify a custom snippet implementation or a results decorator function in your search options.
Is this key-value or full text? For key-value you could use XPath. Any XPath that starts with / or // or fn:collection() or fn:doc() will search the entire database. You can search specific document(s) or collection(s) too.
For full text you'd probably want to use https://docs.marklogic.com/search:search - or possibly https://docs.marklogic.com/cts:search for really low-level control.
There's some example code using search:search from XSL at https://github.com/marklogic/RunDMC which might help. It doesn't use the REST API: it's a traditional form-submit web page. But the view/search.xsl code might give you some idea how to call the search API from XSLT.
That RunDMC code might also help you if you need to call XSL from XQuery: take a look at controller/transform.xqy.