From the previous blog it was apparent that Wikidata could use some additional information concerning amino acids. I added some content, for example which triplet codes for which amino acid (the active L-forms only) and which amino acids are considered to be essential (and have to be taking in via diet). There are also amino acids which are considered to be dispensable in the human body, and are therefore synthesised in the body itself. I wondered in which pathways I could find these non-essential amino acids and did a query on it in Wikidata: SELECT ?ID ?IDLabel (COUNT(DISTINCT ?PWID) AS ?count) WHERE{  ?ID wdt:P279 wd:Q8066 .  ?ID wdt:P279 wd:Q44266770 .   ?PWID wdt:P31 wd:Q4915012 .   ?PWID wdt:P527 ?ID .     SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } } GROUP BY ?ID ?IDLabel ORDER BY DESC(?count) This revealed that there are 5 non essential amino acids, however only 4 can be found in mu...

Yesterday I have been working on annotating a data set, which contained lots of amino acids. For this annotation I made use of the Wikidata database. The fun thing with this database, is that it is very structured. You can do for example SPARQL queries on it (and even though I wasn't familiar with these before I started my PhD, I rather enjoy them now). Below is an example query, which gives all proteinogenic coding L-amino acids (so the active forms of the amino acids, which are being build into proteins through transcription). SELECT ?ID ?IDLabel  WHERE  {    ?ID wdt:P279 wd:Q8066 .    ?ID wdt:P279 wd:Q24301658 .    ?ID wdt:P279 wd:Q3241589 .    SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }  } This gave me 19 results (in 244 ms), and to my surprise there was a mistake in the results: D-isoleucine was labeled as an L-amino acid. So I went in Wikidata again and fixed this issue (which...

Our new intern, who has previously been working on exploring the effect of Short Chain Fatty Acids (SCFA) on muscle energy metabolism, has used PathVisio ( https://www.pathvisio.org/ )  to recreate a pathway! This pathway is described by Canfora et al. (2015) in Nature Review s Endocrinology (DOI:  10.1038/nrendo.2015.128 ). N ot only did this intern link all nodes (Geneproducts, metabolites and pathways/processes) to databases, he also used the software as a tool for graphic design of the pathway that resembles the original Figure in the review paper. This pathway is available on WikiPathways ( http://wikipathways.org/index.php/Pathway:WP4030 ). However, the website displays the pathway slightly different when compared to PathVisio (picture). This visualisation difficulty is being looked at by the WPs developper team. We hope to see many more of these beautiful pathway pictures, since they tell a more complete story!

Hi all, Now that the team is finally back from days off, we can start writing more here (and do some more science, miauw!). For now, we put a lot of work in an AOP information gathering website, which should result in some nice AOP being built before the end of the year (check our portal ). Besides this, lots of manual curation was done on our Pathway collection (check our wiki ). This curation was needed for a poster presentation at the ISMB conference in Prague, where the work of several of our colleagues was presented on shortest path calculations  in a metabolite directed network. For now, we wish you a nice summer and hope you check out our Twitter account.

So, today we  see more student presentations. Lots of talks about SNPs (which are not related to our PhD unfortunately); these BSc students are on their way to becoming MSc students. Two of the talks are related to obesity, a growing epidemic. However, the reasons why certain people become obese, can be caused by small changes in genes (among others, off course). Also, an important Adverse Outcome Pathway(AOP) Telcon took place this morning, in which we proposed an AOP-development strategy. The discussion was very fruitful and the partners of EU-ToxRisk were very positive about the strategy proposal. Soon we will kick off the AOP development, in which BiGCaT will have a supervising and organizing role in the process. On the sidenote, our colleague made a delicious blackberry cheescake . F is famous for her cakes, so we were lucky that we could grab the last couple of slices. We hope that the cake will be digested in a metabolically sound way, not stored as fat-cells, so we are...

Today, we created our own blog, SMaLLCaT, to follow our Open Science Guru (who is also our supervisor) into the online world of communication about science. Guess the name of our research group... BiGCaT! While we are writing our first post, there are bachelor thesis presentations going on. These studentes are on the verge of finishing their bachelor internships. Quite interesting! However, on important matter, F has cake tomorrow! During the break we had an elaborate discussion about a cake we will receive tommorow, because one of our collegeas is invited to give  talk at a conference. The cake will probably consist out of apples, and little black berries that look like raspberries, but aren't. Apparently the english translation for 'bramen' is fairly straight forward... blackberries.. Looking forward to a apple-blackberry cheescake!!