chore: improve the list of prefixes used when building thenanopub, us…

…ing https://schema.org/ instead of http://schema.org/

lib/docs/docs/assets/custom.css

@@ -0,0 +1,4 @@
+/* We use emojis for every bullet lists */
+ul li {
+    list-style-type: none;
+}

lib/docs/docs/cli.md

@@ -70,21 +70,21 @@ np check signed.nanopub.trig
 
 You can generate and enable completions for your shell:
 
-- ZSH
+- 🪐 ZSH
 
     ```bash
     np completions zsh > ~/.zsh/completion/np
     source ~/.zsh/completion/np
     ```
 
-- Bash
+- 🥊 Bash
 
     ```bash
     np completions bash > ~/.bash_completion.d/np
     source ~/.bash_completion.d/np
     ```
 
-- Fish
+- 🐟 Fish
 
     ```bash
     np completions bash > ~/.config/fish/completions/np

lib/docs/docs/index.md

@@ -10,48 +10,29 @@ Whether you're a developer looking to integrate nanopub functionalities into you
 
 ## 🪄 Nanopub management
 
-<ul>
-    <li style="list-style-type: '✍️'">
-        &nbsp;<b>Sign & Publish</b> nanopubs using a RSA private key. Customize your workflow with a <code>profile.yml</code> file.
-    </li>
-    <li style="list-style-type: '🔍'">
-        &nbsp;<b>Verify</b>: ensure the integrity of nanopubs by checking their validity, whether they are signed or unsigned.
-    </li>
-    <li style="list-style-type: '📡'">
-        &nbsp;<b>Fetch</b> nanopubs from the network using their URI.
-    </li>
-</ul>
+- ✍️ **Sign & Publish** nanopublications RDF using a RSA private key. Support for user profile defined in a `profile.yml` file.
+- 🔍 **Verify**: ensure the integrity of nanopubs by checking their validity, whether they are signed or unsigned.
+- 📥 **Fetch** nanopubs from the network using their URI.
 
 ## 📦️ Packaged for multiple interfaces
 
 This library is packaged for easy use across various interfaces and languages:
 
-<ul>
-    <li style="list-style-type: '🦀'">
-        &nbsp;<a href="rust.md"><b>Rust developers</b></a>: available as a Rust crate <code>nanopub</code>.
-    </li>
-    <li style="list-style-type: '🐍'">
-        &nbsp;<a href="python.md"><b>Python programmers</b></a>: available as a Python pip package <code>nanopub-sign</code>.
-    </li>
-    <li style="list-style-type: '🌐'">
-        &nbsp;<a href="javascript.md"><b>Web developers</b></a>: available as a NPM package <code>@nanopub/sign</code>, compiled to <a href="https://webassembly.org/">WebAssembly</a>, for browser integrations with JavaScript, or NodeJS.
-    </li>
-    <li style="list-style-type: '⌨️'">
-        &nbsp;<a href="cli.md"><b>Terminal enthusiasts</b></a>: binary with a Command Line Interface (CLI) for straightforward terminal operations.
-    </li>
-</ul>
+- [🦀 **Rust developers**](rust.md): available as a Rust crate `nanopub`.
+- [🐍 **Python programmers**](python.md): available as a Python pip package `nanopub-sign`.
+- [🌐 **Web developers**](javascript.md): available as a NPM package `@nanopub/sign`, compiled to [WebAssembly](https://webassembly.org/), for browser integrations with JavaScript, or NodeJS.
+- [⌨️  **Terminal enthusiasts**](cli.md): binary with a Command Line Interface (CLI) for straightforward terminal operations.
 
 
 ## ⚔️ Cross-platform support
 
 It runs seamlessly on:
 
-<ul>
-    <li style="list-style-type: '🦊'">&nbsp;Web browsers
-    <li style="list-style-type: '🐧'">&nbsp;Linux
-    <li style="list-style-type: '🍎'">&nbsp;MacOS
-    <li style="list-style-type: '🪟'">&nbsp;Windows
-</ul>
+
+- 🦊 Web browsers
+- 🐧 Linux
+- 🍎 MacOS
+- 🪟 Windows
 
 
 ## 🧩 RDF serialization support
@@ -60,16 +41,10 @@ The library handles most RDF serializations supporting quads, including TriG, Nq
 
 ## 📝 Automated metadata creation
 
-When you sign a nanopub, if it has not already been defined in the pubinfo graph yet:
+When you sign a nanopub some metadata is added, if it has not already been defined in the pubinfo graph:
 
-<ul>
-    <li style="list-style-type: '🕓'">
-        &nbsp;<b>Automatic timestamp</b>: the <code>dct:created</code> attribute is used to add the date and time of creation.
-    </li>
-    <li style="list-style-type: '🪪'">
-        &nbsp;<b>Creator identification</b>: if an ORCID is provided in the profile, it's added using <code>dct:creator</code>. The library also checks for ORCID set with  <code>prov:wasAttributedTo</code> or <code>pav:createdBy</code>.
-    </li>
-</ul>
+- 🕓 **Automatic timestamp**: the `dct:created` attribute is used to add the date and time of creation.
+- 🪪 **Creator identification**: if an ORCID is provided in the profile, it's added using `dct:creator`. The library also checks for ORCID already set with `prov:wasAttributedTo` or `pav:createdBy`.
 
 ## 👆 Interactive playground
 

lib/docs/docs/javascript.md

@@ -75,8 +75,8 @@ Signed Nanopubs can be published to a Nanopub server. This makes the Nanopub acc
 
 Use the `publish` function on a Nanopub, the 2 arguments are optional:
 
-- `profile` is required if you want to also sign the nanopub, it is not required if you provide a signed nanopub
-- If the `server_url` is null it will be published to the test server
+- 🔑 `profile` is required if you want to also sign the nanopub, it is not required if you provide a signed nanopub
+- 🧫 If the `server_url` is null it will be published to the test server
 
 ```typescript
 import { Nanopub, NpProfile } from "@nanopub/sign";
@@ -133,11 +133,11 @@ import init, { Nanopub, NpProfile, KeyPair } from "@nanopub/sign";
 let keypair = new KeyPair();
 keypair = keypair.toJs();
 
-// Create profile with new private key
+// Create a profile with this new private key
 const orcid = "https://orcid.org/0000-0000-0000-0000"
 const profile = new NpProfile(keypair.private, orcid, "Your Name", "");
 
-// Publish nanopub introduction for this profile
+// Publish a nanopub introduction for this profile
 Nanopub.publish_intro(profile, getNpServer(false))
     .then(np => {
         console.log("Published Introduction Nanopub:", np.info());

lib/docs/docs/python.md

@@ -81,8 +81,8 @@ Signed Nanopubs can be published to a Nanopub server. This makes the Nanopub acc
 
 Use the `publish` function on a Nanopub, the 2 arguments are optional:
 
-- `profile` is required if you want to also sign the nanopub, it is not required if you provide a signed nanopub
-- If the `server_url` is null it will be published to the test server
+- 🔑 `profile` is required if you want to also sign the nanopub, it is not required if you provide a signed nanopub
+- 🧫 If the `server_url` is null it will be published to the test server
 
 ```python
 from nanopub_sign import Nanopub, NpProfile, get_np_server
@@ -146,15 +146,15 @@ from nanopub_sign import Nanopub, NpProfile, KeyPair, get_np_server
 # Randomly generate a new private/public key pair
 keypair = KeyPair()
 
-# Create profile with new private key
+# Create a profile with this new private key
 new_profile = NpProfile(
     private_key=keypair.private,
     orcid_id="https://orcid.org/0000-0000-0000-0000",
     name="",
     introduction_nanopub_uri=""
 )
 
-# Publish nanopub introduction for this profile
+# Publish a nanopub introduction for this profile
 np = Nanopub.publish_intro(new_profile, get_np_server())
 print(np.info())
 

lib/docs/docs/rust.md

@@ -49,7 +49,7 @@ let signed_np = Nanopub::new(np_rdf).unwrap().sign(&profile).unwrap();
 let checked_np = Nanopub::new(&signed_np.rdf().unwrap()).unwrap().check();
 
 // Publish is async
-let rt = runtime::Runtime::new().expect("Failed to create Tokio runtime");
+let rt = runtime::Runtime::new().expect("Runtime failed");
 
 let published_np = rt.block_on(async {
     Nanopub::new(np_rdf).unwrap().publish(Some(&profile), None).await.unwrap()
@@ -61,8 +61,8 @@ println!("{}", published_np)
 
 The `publish` function takes 2 optional arguments:
 
-- `profile` is required if you want to also sign the nanopub, it is not required if you provide a signed nanopub
-- If the `server_url` is none it will be published to the test server
+- 🔑 `profile` is required if you want to also sign the nanopub, it is not required if you provide a signed nanopub
+- 🧫 If the `server_url` is none it will be published to the test server
 
 > Provide the nanopub signed or unsigned:
 >
@@ -119,14 +119,37 @@ The `fetch` static function on the `Nanopub` struct allows you to retrieve Nanop
 use nanopub::{Nanopub, NpProfile, NpError};
 use tokio::runtime;
 
-let url = "https://w3id.org/np/RAltRkGOtHoj5LcBJZ62AMVOAVc0hnxt45LMaCXgxJ4fw";
-let rt = runtime::Runtime::new().expect("Failed to create Tokio runtime");
+let uri = "https://w3id.org/np/RAltRkGOtHoj5LcBJZ62AMVOAVc0hnxt45LMaCXgxJ4fw";
+let rt = runtime::Runtime::new().expect("Runtime failed");
 
 let np = rt.block_on(async {
-    Nanopub::fetch(&url).await
+    Nanopub::fetch(&uri).await
 }).unwrap();
 ```
 
+
+### 🔑 Generate private key and publish introduction
+
+You can generate a new private/public key pair, and publish a nanopub introduction to register this key under your ORCID in the Nanopublications network:
+
+```rust
+use nanopub::{profile::gen_keys, Nanopub, NpProfile};
+use tokio::runtime;
+
+// Randomly generate a new private/public key pair
+let (private_key, _pubkey) = gen_keys().unwrap();
+
+// Create a profile with this new private key
+let profile = NpProfile::new(&private_key, "https://orcid.org/0000-0000-0000-0000", "", None).unwrap();
+
+// Publish a nanopub introduction for this profile
+let rt = runtime::Runtime::new().expect("Runtime failed");
+let np = rt.block_on(async {
+    Nanopub::new_intro(&profile).unwrap()
+        .publish(Some(&profile), None).await.unwrap();
+});
+```
+
 ## 📖 API reference
 
 Checkout the **[API documentation](https://docs.rs/nanopub)** for more details on how to use the different components and functions of the rust crate.

lib/docs/includes/abbreviations.md

@@ -6,6 +6,7 @@
 *[OSI]: Open Source Initiative
 *[FSF]: Free Software Foundation
 *[CVE]: Common Vulnerabilities and Exposures
+*[WSL]: Windows Subsystem Linux
 *[LLM]: Large Language Model
 *[LLMs]: Large Language Models
 *[ML]: Machine Learning

lib/docs/mkdocs.yml

@@ -20,14 +20,14 @@ theme:
     - media: "(prefers-color-scheme: light)"
       scheme: default
       primary: lime
-      accent: indigo
+      accent: deep orange
       toggle:
         icon: material/weather-night
         name: Switch to dark mode
     - media: "(prefers-color-scheme: dark)"
       scheme: slate
       primary: lime
-      accent: indigo
+      accent: deep orange
       toggle:
         icon: material/weather-sunny
         name: Switch to light mode

lib/src/lib.rs

@@ -34,7 +34,7 @@ pub use error::NpError;
 ///
 /// let signed_np = Nanopub::new(&np_rdf).unwrap().sign(&profile).unwrap();
 /// let checked_np = Nanopub::new(&signed_np.rdf().unwrap()).unwrap().check();
-/// let rt = runtime::Runtime::new().expect("Failed to create Tokio runtime");
+/// let rt = runtime::Runtime::new().expect("Runtime failed");
 /// let published_np = rt.block_on(async {
 ///   Nanopub::new(&np_rdf).unwrap().publish(Some(&profile), None).await.unwrap()
 /// });

lib/src/nanopub.rs

@@ -85,7 +85,7 @@ impl Nanopub {
     /// use nanopub::Nanopub;
     /// use tokio::runtime;
     /// let url = "https://w3id.org/np/RAltRkGOtHoj5LcBJZ62AMVOAVc0hnxt45LMaCXgxJ4fw";
-    /// let rt = runtime::Runtime::new().expect("Failed to create Tokio runtime");
+    /// let rt = runtime::Runtime::new().expect("Runtime failed");
     ///
     /// let np = rt.block_on(async {
     ///   Nanopub::fetch(&url).await
@@ -353,7 +353,7 @@ impl Nanopub {
     /// let np_rdf = fs::read_to_string("./tests/resources/simple1-rsa.trig").unwrap();
     /// let orcid = "https://orcid.org/0000-0000-0000-0000";
     /// let profile = NpProfile::new(&private_key, orcid, "", None).unwrap();
-    /// let rt = runtime::Runtime::new().expect("Failed to create Tokio runtime");
+    /// let rt = runtime::Runtime::new().expect("Runtime failed");
     ///
     /// let np = rt.block_on(async {
     ///   Nanopub::new(&np_rdf).unwrap().publish(Some(&profile), None).await
@@ -472,7 +472,7 @@ impl Nanopub {
     /// let private_key = "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";
     /// let orcid = "https://orcid.org/0000-0000-0000-0000";
     /// let profile = NpProfile::new(&private_key, orcid, "User Name", None).unwrap();
-    /// let rt = runtime::Runtime::new().expect("Failed to create Tokio runtime");
+    /// let rt = runtime::Runtime::new().expect("Runtime failed");
     ///
     /// let np = rt.block_on(async {
     ///   Nanopub::new_intro(&profile).unwrap().publish(Some(&profile), None).await.unwrap()

lib/src/utils.rs

@@ -15,6 +15,7 @@ use crate::error::NpError;
 /// Parse RDF from various format to a `LightDataset` (trig, nquads, JSON-LD)
 pub fn parse_rdf(rdf: &str) -> Result<LightDataset, NpError> {
     let rdf = rdf.to_string();
+    // NOTE: an efficient way to differentiate between JSON-LD and TriG is to check if the string starts with '{' or '['
     let dataset = if rdf.trim().starts_with('{') || rdf.trim().starts_with('[') {
         parse_jsonld(&rdf)?
     } else {
@@ -87,7 +88,7 @@ pub fn ns(ns: &str) -> Namespace<String> {
 
 // TODO: improve to extract prefixes from the input RDF
 /// Get the prefixes of a Nanopub
-pub fn get_prefixes(np_uri: &str, np_ns: &str) -> [(Prefix<String>, Iri<String>); 14] {
+pub fn get_prefixes(np_uri: &str, np_ns: &str) -> [(Prefix<String>, Iri<String>); 18] {
     [
         (
             Prefix::new_unchecked("this".to_string()),
@@ -109,23 +110,30 @@ pub fn get_prefixes(np_uri: &str, np_ns: &str) -> [(Prefix<String>, Iri<String>)
             Prefix::new_unchecked("xsd".to_string()),
             Iri::new_unchecked("http://www.w3.org/2001/XMLSchema#".to_string()),
         ),
-        // TODO: use https:// by default?
         (
-            Prefix::new_unchecked("schema".to_string()),
-            Iri::new_unchecked("http://schema.org/".to_string()),
-        ),
-        (
-            Prefix::new_unchecked("foaf".to_string()),
-            Iri::new_unchecked("http://xmlns.com/foaf/0.1/".to_string()),
+            Prefix::new_unchecked("owl".to_string()),
+            Iri::new_unchecked("http://www.w3.org/2002/07/owl#".to_string()),
         ),
         (
-            Prefix::new_unchecked("biolink".to_string()),
-            Iri::new_unchecked("https://w3id.org/biolink/vocab/".to_string()),
+            Prefix::new_unchecked("skos".to_string()),
+            Iri::new_unchecked("http://www.w3.org/2004/02/skos/core#".to_string()),
         ),
         (
             Prefix::new_unchecked("np".to_string()),
             Iri::new_unchecked(ns("np").to_string()),
         ),
+        (
+            Prefix::new_unchecked("npx".to_string()),
+            Iri::new_unchecked(ns("npx").to_string()),
+        ),
+        (
+            Prefix::new_unchecked("dc".to_string()),
+            Iri::new_unchecked("http://purl.org/dc/elements/1.1/".to_string()),
+        ),
+        (
+            Prefix::new_unchecked("dcterms".to_string()),
+            Iri::new_unchecked("http://purl.org/dc/terms/".to_string()),
+        ),
         (
             Prefix::new_unchecked("prov".to_string()),
             Iri::new_unchecked("http://www.w3.org/ns/prov#".to_string()),
@@ -135,16 +143,24 @@ pub fn get_prefixes(np_uri: &str, np_ns: &str) -> [(Prefix<String>, Iri<String>)
             Iri::new_unchecked("http://purl.org/pav/".to_string()),
         ),
         (
-            Prefix::new_unchecked("dcterms".to_string()),
-            Iri::new_unchecked("http://purl.org/dc/terms/".to_string()),
+            Prefix::new_unchecked("schema".to_string()),
+            Iri::new_unchecked("https://schema.org/".to_string()),
+        ),
+        (
+            Prefix::new_unchecked("foaf".to_string()),
+            Iri::new_unchecked("http://xmlns.com/foaf/0.1/".to_string()),
         ),
         (
             Prefix::new_unchecked("orcid".to_string()),
             Iri::new_unchecked("https://orcid.org/".to_string()),
         ),
         (
-            Prefix::new_unchecked("npx".to_string()),
-            Iri::new_unchecked(ns("npx").to_string()),
+            Prefix::new_unchecked("biolink".to_string()),
+            Iri::new_unchecked("https://w3id.org/biolink/vocab/".to_string()),
+        ),
+        (
+            Prefix::new_unchecked("infores".to_string()),
+            Iri::new_unchecked("https://w3id.org/biolink/infores/".to_string()),
         ),
     ]
 }