If you have ridden any train in Tokyo since 2016, you have come across station number signage like the picture above. In the run up to the 2020 Tokyo Olympics Japanese transit companies nationwide have been busy implementing station numbering and installing new signage everywhere.
JR East implemented the largest Japanese station numbering scheme in October 2016. All JR Tokyo train lines have 2 letter codes combined with long-established train line colors:Major stations have three letter codes:
The entire package looks like this:
Station numbering might look good on paper but the reality in a major station like Shinjuku, the world’s busiest train station, is confusing.
A major weak point of station numbering is that users are presented with a bunch of different station numbers when several different line converge at a station point. The Shinjuku station number changes with each line on each platform:
Each platform has its own different numbering as well:

The different station numbers for Shinjuku are unified by the three-letter SJK Shinjuku station code.

But if the station does not have a three-letter code, all you get are a bunch of different, separate station numbers, such as Nagano station, a small but frustrating transfer point.
Of the major digital Japan map services (Apple, Google and Yahoo Japan) only Apple goes all in with station numbering and train line codes. Google and Yahoo Japan don’t use them at all.
This is very apt, Yahoo Japan and Google focus on features Japanese users like while Apple focuses on features that appeal more to international users than Japanese users. Here is a comparison of the same transit trip on Yahoo Japan, Google and Apple:
(Note that Yahoo Japan puts in extra effort to show fare of each transfer point and which car to ride to be nearest the destination exit, nice touches)
Real communication or sowing seeds of misunderstanding?
Station numbering is 1980s era thinking, a time when most of the signage was Japanese with English an after thought, if at all. In today’s Japan we have English everywhere. We also have smartphones, Google Translate, multilingual train announcements and multilingual electronic info screens on trains and subways:

The real problem is that station numbers and train codes lull international visitors into thinking that Japanese know and use them. They don’t.
Listen carefully on a Tokyo train and you will notice station numbers are not used in Japanese announcements, only in the English ones. Station numbers and train line codes mean nothing to the average Japanese person, they exist in a hot house bubble with no connection to real world use.
As the Japanese blog Memory is a Person points out, if a foreigner asks, “How can I get to the JA line?” a Japanese person will invariably assume they want the nearest JR line. OSK will be mistaken for Osaka, and so on.
In other words, station numbers, station codes and train codes end up creating the very problem they were designed to solve: confusion.
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