Introduction to Cheminformatic Law

I want to change the nature of the lecture occasionally where it would be useful for students to know the basics of law and how it applies into chemistry. Knowing how to do things, what forms to fill out, and how to mine legal data is a valuable skill for any cheminformatician. I have found it very useful and eventually we will move into something called patent informatics.

Let’s first introduce the basics: Copyrights, Trademarks, and Patents.

• Copyright: A copyright is a literary work or perhaps even some software code like an algorithm that is creative. It protects the rights of the person that authored that work. For example, for music composition if your music was performed elsewhere you can collect performance royalties.
• Trademarks: A trademark is a unique identifier to the entity like a logo design or slogan. For example, the Nike Inc. tick mark with slogan “Just Do It” is a trademark under them as a marketing brand.
• Patent: A patent will protect a new discoveries, methods, and different compositions of matter (medicine). For example, anti-venom for snake bites are chemicals that are patented.

I’ll first tell you my experience and in the next blog post I will then teach you how to do it.

Personal Story

I wanted to file my software package Global-Chem as an intellectual piece of code. I wrote a little graph algorithm I thought was cool that builds the network based on the directory tree. I thought the way I wrote Global-Chem was an intellectual work because a lot of those entries I curated over time. It felt like it belonged to me even if some if it might be wrong. Here is an example of the named reaction list I was curating.

'aza-wittig_reaction': r'CP(C)(C)=NC.CC(C)=O.C/C(C)=N/C', # with ketone to imine, with CO2 to isocyanate, with CS2 to isothiocyanate, with H2O to primary amine (=staudinger),…
'meisenheimer_rearrangement': '[O-][N+](C)(C)C.CN(OC)C', # [1,2] rearrangement, [O-][N+](C)(C(C)C=C)C.CN(OC/C=C/C)[2,3] rearrangement
'staudinger_reaction': 'CP(C)(C)=NC.CN', # = aza-wittig with H2O
'diels-alder_cycloaddition': 'C=CC=C.C=C.C1=CCCCC1'

However, what I submitted was the code used to call the data which I found to be unique in terms of my own style of trying to write a Node network:

Rules:
   1.) There must be a connection from one node to the next. Nodes in space cannot exist.
Algorithm:
   1.) First Find the Node in the Network
   2.) Add the Child to the Parent
   3.) Add the Child to the Network
   4.) Add the Parent to the Child
   5.) Add the Parent to the Network
Graph Algorithm:
   O(c): Child Node
   O(p): Parent Node
   N: Network
   1.) O(p) <---- N
   2.) O(c) <---- O(p)
   3.) O(c) <---- N
   4.) O(p) ----> O(c)
   5.) O(p) ----> N

I submitted both the code and the doc-string to the U.S Copyright office and after 2 months I received:

A denial on my work. The code was open sourced and licensed under Mozilla Public License (MPL) or it was presented in a reasonable manner.

When you receive a denial it doesn’t mean we need to pay up a fee of $350.00 and file the appeal. We can be smart. I decided to change the nature of the presentation of my work in the form of a book. What I did is first convert all of the network into a tsvfile:

def to_tsv(self, out_file = 'global_chem.tsv'):

    master_category_keys = {
        'organic_chemistry': ['narcotics', 'organic_synthesis', 'medicinal_chemistry', 'proteins', 'miscellaneous'],
        'environmental_chemistry': ['environment', 'interstellar_space'],
        'materials_chemistry': ['materials'],
        'pharmaceutical_sciences': ['formulation']
    }

    out_file = open(out_file, 'w')
    all_nodes = self.get_all_nodes()
    for node in all_nodes:
        node_name = node.name
        tree_path = node.__module__
        category = ''
        sub_category = tree_path.split('.')[1]

        for key, value in master_category_keys.items():
            if sub_category in value:
                category = key
        
       for key, value in node.get_smiles().items():
           out_file.write(f'{key}\t{value}\t{node_name}\t{category}\t{tree_path}\n')

    out_file.close()

I then loaded it into Google Drive and copied the data over into a Google Doc. I added Table of Contents and Headers and Made it a book of Common Chemical Names to SMILES.

Which is now copyrighted under my name. This was kind of test to see what I can and cannot do but also I wanted to formulate my work into a standard.

In the next section for Cheminformatic Law, I will walk through the process of copywriting and trademarking.