Agreed. However, there is a lot of knowledge which is easy to structure. Examples: minerals, crystals, chemical substances, chemical reactions, biological species, genes, proteins, metabolic pathways, biological cell types, astronomical objects, geographical / geological objects, archaeological findings, demographical data (including historical)...
In practice we need a mixture of structured and unstructured (like regular Wikipedia) information.
There no real reason why proteins and acheological findings should be in the same database.
genes, proteins
Uniprot with both Swissprot and Trembl works well.
minerals, crystals, chemical substances
PubChem is in principle a good way to store information about chemical substances.
I don’t know much about crystals but do we need a database about them, that separate from PubChem?
From what I heard the data quality of PubChem isn’t ideal. But that not a problem easily solved by creating a new database.
I don’t know much about astrophysics, but I would be surprised if those folks have enough money to buy all those telescopes but not enough money to have a good database of astronomical objects.
geographical / geological objects,
OpenStreetMap is open data for geography. Do you think it lacks something?
http://www.obofoundry.org/ also provides nice information. In bioinformatics there are plenty of people who care about organising databases of knowledge that’s easy to structure.
archaeological findings,
I have no idea on that front. It could be that the related academics don’t use computer enough to have a decent database.
demographical data (including historical)
I don’t know of the correct source, but there probably a lot of complicated copyright involved. Different definition of terms are also complicating things. Illegal drug sales got recently added to the [British GDP] (http://marginalrevolution.com/marginalrevolution/2014/02/improving-gdp.html). Having a database that makes it easy to compare numbers won’t be easy.
Great links, thanks! The situation looks much better than I assumed.
I don’t know much about crystals but do we need a database about them, that separate from PubChem?
Probably not separate. However, it seems that PubChem doesn’t store data about crystal structure, unless I’m missing something (I looked at the entries for SiO2 and NaCl)? Also, PubChem doesn’t seem to have lots of data about reactions.
OpenStreetMap is open data for geography. Do you think it lacks something?
For geography it’s probably good, but it doesn’t seem to have much data about geology, unless I’m missing something? The latter would require some sort of a 3D map of the Earth crust.
In general in the last decade a lot of people in the bioinformatics community tried to find solutions to problems in that sphere.
People like Barry Smith did a lot of work on ontology and we know have bioinformatics driven ontology for emotions because they psychologists just don’t work on that level. When it comes to what the psychologists themselves produce they are stuck with utter crap like the DSM-5. The DSM get’s produced by the American Psychological Association.
PubChem is probably reasonble good where it touches areas that bioinformatics is interested in but crystals aren’t in that sphere.
A lot of information about chemicals that’s out there is also intellectual property of big pharma companies who aren’t happen with sharing it in a open fashion. The American Chemical Society fought against PubChem being well funded.
It an interesting pattern. Bioinformatics might work preceisely because it has no huge society of bioinformaticians that can hold back scientific process in the way the association of the chemists and psychologists do.
For geography it’s probably good, but it doesn’t seem to have much data about geology, unless I’m missing something? The latter would require some sort of a 3D map of the Earth crust.
I don’t know exactly, but I think if the data is available it should go somewhere in that project.
Agreed. However, there is a lot of knowledge which is easy to structure. Examples: minerals, crystals, chemical substances, chemical reactions, biological species, genes, proteins, metabolic pathways, biological cell types, astronomical objects, geographical / geological objects, archaeological findings, demographical data (including historical)...
In practice we need a mixture of structured and unstructured (like regular Wikipedia) information.
There no real reason why proteins and acheological findings should be in the same database.
Uniprot with both Swissprot and Trembl works well.
PubChem is in principle a good way to store information about chemical substances. I don’t know much about crystals but do we need a database about them, that separate from PubChem?
From what I heard the data quality of PubChem isn’t ideal. But that not a problem easily solved by creating a new database.
http://eol.org/
I don’t know much about astrophysics, but I would be surprised if those folks have enough money to buy all those telescopes but not enough money to have a good database of astronomical objects.
OpenStreetMap is open data for geography. Do you think it lacks something?
I think there are databases for those things http://en.wikipedia.org/wiki/List_of_biological_databases#Metabolic_pathway_and_Protein_Function_databases lists a bunch.
http://www.obofoundry.org/ also provides nice information. In bioinformatics there are plenty of people who care about organising databases of knowledge that’s easy to structure.
I have no idea on that front. It could be that the related academics don’t use computer enough to have a decent database.
I don’t know of the correct source, but there probably a lot of complicated copyright involved. Different definition of terms are also complicating things. Illegal drug sales got recently added to the [British GDP] (http://marginalrevolution.com/marginalrevolution/2014/02/improving-gdp.html). Having a database that makes it easy to compare numbers won’t be easy.
Great links, thanks! The situation looks much better than I assumed.
Probably not separate. However, it seems that PubChem doesn’t store data about crystal structure, unless I’m missing something (I looked at the entries for SiO2 and NaCl)? Also, PubChem doesn’t seem to have lots of data about reactions.
For geography it’s probably good, but it doesn’t seem to have much data about geology, unless I’m missing something? The latter would require some sort of a 3D map of the Earth crust.
In general in the last decade a lot of people in the bioinformatics community tried to find solutions to problems in that sphere.
People like Barry Smith did a lot of work on ontology and we know have bioinformatics driven ontology for emotions because they psychologists just don’t work on that level. When it comes to what the psychologists themselves produce they are stuck with utter crap like the DSM-5. The DSM get’s produced by the American Psychological Association.
PubChem is probably reasonble good where it touches areas that bioinformatics is interested in but crystals aren’t in that sphere.
A lot of information about chemicals that’s out there is also intellectual property of big pharma companies who aren’t happen with sharing it in a open fashion. The American Chemical Society fought against PubChem being well funded.
It an interesting pattern. Bioinformatics might work preceisely because it has no huge society of bioinformaticians that can hold back scientific process in the way the association of the chemists and psychologists do.
I don’t know exactly, but I think if the data is available it should go somewhere in that project.