Merge pull request #44 from jcuadros/jc_contribution_1

Contribution: Using InChI and InChIKey to Annotate your Chemical Entities - resubmission Accepted!

book/contributions/rec_using_inchi/recipes/rec_using_inchi.md

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+# Using InChI and InChIKey to annotate your chemical entities 
+
+```{dropdown} About this interactive ![icons](../static/img/rocket.png) recipe
+- Author: [Jordi Cuadros](https://orcid.org/0000-0001-6513-9140)
+- Reviewer:
+- Topics: InChI, InChIKey
+- Format: Tutorial
+- Scenarios: Retrieve the InChI and InChIKey of a chemical
+- Skills:
+    - Understand what an InChI is ([IUPAC](http://publications.iupac.org/ci/2006/2806/2806-pp12-15.pdf), [InChI-Trust](https://www.inchi-trust.org/))
+    - Know what MOL files are and where to get them ([Wikipedia](https://en.wikipedia.org/wiki/Chemical_table_file),
+ [Dassault Systèmes] (https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf))
+    - Understand what a SMILES string is ([Wikipedia](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system),
+[OpenSMILES](http://opensmiles.org/))
+- Learning outcomes: After completing this example you should understand:
+    - What makes InChI and InChIKey convenient identifier for chemical
+    - How to obtain the InChI and the InChIKey of a chemical
+    - How to identify a chemical behind an InChI or an InChIKey
+- Citation: 'Using InChI and InChIKey to annotate your chemical entities', The IUPAC FAIR Chemistry Cookbook,
+ https://iupac.github.io/WFChemCookbook/recipes/rec_using_inchi.html
+- Reuse: This notebook is made available under a [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.
+```
+
+## Scenario
+
+So far, we are quite used to identifying chemical substances with a name, a drawing or a CAS Registry Number (CAS-RN).
+However, these identifiers have some issues that affect their usability for indexing and searching.
+A way to increase the FAIRness of our documents is to annotate our chemical substances with InChI and InChiKeys, either in papers, data, or metadata files.
+
+Let's do it together!
+
+## Case 1: I can draw my chemical substance accurately
+
+Many molecular drawing packages like [ChemDraw](https://revvitysignals.com/products/research/chemdraw),
+[ChemSketch](https://www.acdlabs.com/products/chemsketch/), or [MarvinSketch](https://chemaxon.com/marvin),
+can output the InChI and the InChIKey for a molecule drawn on them. Other drawing packages such as the ones listed on the
+[Wikipedia page on molecule editors](https://en.wikipedia.org/wiki/Molecule_editor) may also be helpful.
+
+![](../images/rec_using_inchi_fig1.png)
+
+Alternatively, we can use the [CACTUS Chemical Identifier Resolver](https://cactus.nci.nih.gov/chemical/structure)
+to get the InChI or the InChIKey of a drawn chemical.
+
+![](../images/rec_using_inchi_fig2.png)
+
+## Case 2: I can unambiguously name my chemical 
+
+If we can name our chemical (and this name is included in the chemical databases), 
+you can use PubChem or ChemSpider searching features, or the 
+[CACTUS Chemical Identifier Resolver](https://cactus.nci.nih.gov/chemical/structure), to obtain the InChI or the InChIKey.
+
+![](../images/rec_using_inchi_fig3.png)
+
+If you can name the compound according to IUPAC systematic nomenclature, you can use the 
+[Open Parser for Systematic IUPAC nomenclature (OPSIN)](https://opsin.ch.cam.ac.uk/index.html),
+to calculate (this is not a search) the InChI and the InChiKey. OPSIN can be downloaded or accessed online.
+
+![](../images/rec_using_inchi_fig4.png)
+
+## Case 3: I have a MOL file for my chemical
+
+If you have a [MOL or SDF file](https://en.wikipedia.org/wiki/Chemical_table_file) for your molecule, you can use the 
+[UniChem service](https://www.ebi.ac.uk/unichem/) to upload the file and obtain its InChI and InChIKey.
+
+You can also use the following software that you install locally to process the MOL file:
+
+-   [InChI core software](https://www.inchi-trust.org/download-latest-inchi-standard-software/).
+-   [OpenBabel](https://openbabel.org/wiki/Main_Page),
+
+to convert a MOL file to InChI or InChIKey.
+
+Many common molecular drawing programs can also export and import MOL files. 
+This way. they can also be used to convert a MOL file to an InChI or InChIKey. 
+Make sure to check that isotope and stereochemistry information is preserved when importing and exporting MOL files.
+
+## Case 4: I have the SMILES string or the InChI for my chemical
+
+In the case you are able to write our chemical as a [SMILES](https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system) 
+string or already have an InChI and just need the InChIKey for it, we may use the
+[CACTUS Chemical Identifier Resolver](https://cactus.nci.nih.gov/chemical/structure).
+
+![](../images/rec_using_inchi_fig5.png)
+
+![](../images/rec_using_inchi_fig6.png)
+
+Please be aware that complex InChIs can not be interpreted by the CACTUS Chemical Identifier Resolver.
+
+Again, import and export features of the common molecular drawing packages may be useful in this case. 
+Last but not least, databases can also help find an InChI or an InChIKey from a SMILES; provided the compound is included in the database. 
+Remember to check the responses before taking them as correct (specially for stereochemistry and isotope distribution).
+
+## Case 5: I only have the CAS Registry Number (CAS-RN) for my chemical
+
+If you only have the [CAS Registry Number (CAS-RN)](https://www.cas.org/cas-data/cas-registry) for your chemical,
+you have to resort to a database to potentially find the InChI and InChIKey.
+Curated chemical databases, such as the [ACS Common Chemistry service](https://commonchemistry.cas.org/) (for common chemicals) or 
+[SciFinder](https://scifinder.cas.org), will be among the first options to try.
+Other databases like [PubChem](https://pubchem.ncbi.nlm.nih.gov), [ChemSpider](https://chemspider.com), [Wikidata](https://www.wikidata.org/),
+or [Wikipedia](https://www.wikipedia.org/) (quote your CAS-RN when searching) may also work in many cases for common chemicals.
+
+![](../images/rec_using_inchi_fig7.png)
+
+## Last step: Let's check our InChI and InChIKey
+
+Once you have found the InChI and the InChIKey of a chemical species, it may be worth double-checking what you got as a result.
+
+### Quick checks
+
+Let's start with some simple checks.
+
+- Does the InChI starts with the expected characters, "InChI=1S/"?
+- Does the InChI have the expected layers, e.g., t, m, s sublayers if you are referring to a specific isomer, or i if you have an isotopically -labelled compound?
+- Does the InChIKey have 27 characters?
+- Does it follow the expected structure 14 uppercase letters, a hyphen, 10 uppercase letters, a hyphen and one last uppercase letter?
+- Does it end with N if the chemical species is neutral?
+- Does the InChIKey has SA has the last two letters preceding the second dash? (SA there means version 1 standard)
+
+### Import your InChI into a molecular drawing tool
+
+You can use your preferred molecular drawing tool to import the InChI and check that the response corresponds to your chemical structure.
+The drawing tool at [UniChem](https://www.ebi.ac.uk/unichem/) may well serve this purpose.
+
+![](../images/rec_using_inchi_fig8.png)
+
+### Google it!
+
+Major web search engines, like Google, Bing or Baidu can search from an InChIKey; its structure is largely specific and allows finding 
+references and data related to your chemical specie. So, search your InChIKey and make sure you get back responses that belong to your molecule.
+
+### Use an InChI resolver
+
+Last, specific tools are being developed to resolve InChI and InChIKey by searching into databases. 
+Currently, InChI and InChIKey resolution can be done at [PubChem search page](https://pubchem.ncbi.nlm.nih.gov/), [UniChem](https://www.ebi.ac.uk/unichem/),
+or the [CACTUS Chemical Identity Resolver](https://cactus.nci.nih.gov/chemical/structure).
+
+An API to resolve programmatically InChIKeys are also being developed. Progress can be checked out at [InChI Resolver](https://inchi-resolver.org/).
+